rs9377619

Variant names:

• chr6-104145992-A-G
• rs9377619

Variant summary

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

The variant allele was found at a frequency of 0.119 in 152,206 control chromosomes in the GnomAD database, including 1,267 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 (1267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18184 AN: 152088 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.119 AC: 18179 AN: 152206 Hom.: 1267 Cov.: 32 AF XY: 0.122 AC XY: 9047 AN XY: 74402

African (AFR) AF: 0.0515 AC: 2142 AN: 41556

American (AMR) AF: 0.139 AC: 2120 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.119 AC: 618 AN: 5178

South Asian (SAS) AF: 0.201 AC: 968 AN: 4822

European-Finnish (FIN) AF: 0.108 AC: 1140 AN: 10602

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10105 AN: 67990

Other (OTH) AF: 0.160 AC: 337 AN: 2108

Alfa AF: 0.139 Hom.: 3333

Bravo AF: 0.118

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.79
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs9377619; hg19: chr6-104593867; COSMIC: COSV60261622;