rs3868143

Variant names:

• chr16-67294550-T-C
• rs3868143
• NM_001100915.3:c.1590+30A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-67294550-T-C
• chr16-67294550-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001100915.3(KCTD19):​c.1590+30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,494,894 control chromosomes in the GnomAD database, including 18,837 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (7686 hom., cov: 32)
  • Exomes 𝑓: 0.094 (11151 hom.)
• Consequence: KCTD19 NM_001100915.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 19 publications found

Genes affected

KCTD19 (HGNC:24753): (potassium channel tetramerization domain containing 19) Predicted to be involved in protein homooligomerization. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCTD19	NM_001100915.3	c.1590+30A>G		intron_variant	Intron 11 of 15	ENST00000304372.6	NP_001094385.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCTD19	ENST00000304372.6	c.1590+30A>G		intron_variant	Intron 11 of 15	1	NM_001100915.3	ENSP00000305702.5
KCTD19	ENST00000570049.5	n.3422+30A>G		intron_variant	Intron 11 of 15	1
KCTD19	ENST00000566392.5	n.2859+30A>G		intron_variant	Intron 10 of 14	2
KCTD19	ENST00000569333.5	n.3588+30A>G		intron_variant	Intron 9 of 13	2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33856 AN: 152024 Hom.: 7649 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.169

GnomAD2 exomes AF: 0.119 AC: 29444 AN: 248402 AF XY: 0.115

Gnomad AFR exome AF: 0.595

Gnomad AMR exome AF: 0.0659

Gnomad ASJ exome AF: 0.0687

Gnomad EAS exome AF: 0.00390

Gnomad FIN exome AF: 0.141

Gnomad NFE exome AF: 0.0786

Gnomad OTH exome AF: 0.0960

GnomAD4 exome AF: 0.0940 AC: 126188 AN: 1342752 Hom.: 11151 Cov.: 21 AF XY: 0.0937 AC XY: 63172 AN XY: 674108

African (AFR) AF: 0.608 AC: 19017 AN: 31268

American (AMR) AF: 0.0699 AC: 3107 AN: 44434

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 1813 AN: 25396

East Asian (EAS) AF: 0.00263 AC: 103 AN: 39156

South Asian (SAS) AF: 0.148 AC: 12417 AN: 83824

European-Finnish (FIN) AF: 0.140 AC: 7443 AN: 53228

Middle Eastern (MID) AF: 0.154 AC: 854 AN: 5544

European-Non Finnish (NFE) AF: 0.0747 AC: 74956 AN: 1003512

Other (OTH) AF: 0.115 AC: 6478 AN: 56390

GnomAD4 genome AF: 0.223 AC: 33939 AN: 152142 Hom.: 7686 Cov.: 32 AF XY: 0.221 AC XY: 16466 AN XY: 74378

African (AFR) AF: 0.584 AC: 24231 AN: 41470

American (AMR) AF: 0.112 AC: 1720 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3468

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5182

South Asian (SAS) AF: 0.143 AC: 688 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1556 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0740 AC: 5033 AN: 68002

Other (OTH) AF: 0.167 AC: 354 AN: 2114

Alfa AF: 0.113 Hom.: 1513

Bravo AF: 0.233

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.36
DANN	Benign	0.38
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3868143; hg19: chr16-67328453; COSMIC: COSV58572555; COSMIC: COSV58572555;