rs738842

Variant names:

• chr22-16579276-T-C
• rs738842
• ENST00000493696.2:n.679-1203A>G

Variant summary

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

The ENST00000493696.2(KCNMB3P1):​n.679-1203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,162 control chromosomes in the GnomAD database, including 3,697 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 0.21 (3697 hom., cov: 33)
• Consequence: KCNMB3P1 ENST00000493696.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

KCNMB3P1 (HGNC:6288): (KCNMB3 pseudogene 1)

ENSG00000290416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNMB3P1	ENST00000493696.2	n.679-1203A>G		intron_variant	Intron 2 of 2	6
ENSG00000290416	ENST00000725389.1	n.385-1203A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31350 AN: 152044 Hom.: 3694 Cov.: 33

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.209

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.206 AC: 31357 AN: 152162 Hom.: 3697 Cov.: 33 AF XY: 0.208 AC XY: 15478 AN XY: 74380

African (AFR) AF: 0.0751 AC: 3118 AN: 41534

American (AMR) AF: 0.241 AC: 3683 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5176

South Asian (SAS) AF: 0.194 AC: 937 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2796 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18163 AN: 67964

Other (OTH) AF: 0.207 AC: 438 AN: 2116

Alfa AF: 0.237 Hom.: 563

Bravo AF: 0.200

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.83
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs738842; hg19: chr22-17060166;