rs16882214

Positions:

• chr6-19443704-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.123 in 152,170 control chromosomes in the GnomAD database, including 1,555 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 0.12 (1555 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19443704C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNC-LBCS	ENST00000636202.1	n.852-46167G>C		intron_variant		5
LNC-LBCS	ENST00000653002.1	n.1036+91183G>C		intron_variant
LNC-LBCS	ENST00000660410.1	n.883-80880G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18768 AN: 152052 Hom.: 1551 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.123 AC: 18782 AN: 152170 Hom.: 1555 Cov.: 33 AF XY: 0.132 AC XY: 9823 AN XY: 74388

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.122

Alfa AF: 0.136 Hom.: 206

Bravo AF: 0.115

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.17
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16882214; hg19: chr6-19443935;