chr6-103036537-A-C

Variant names:

• chr6-103036537-A-C
• rs9390939

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 0.267 in 151,886 control chromosomes in the GnomAD database, including 5,791 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 0.27 (5791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 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: 0.267 AC: 40504 AN: 151768 Hom.: 5794 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.267 AC: 40503 AN: 151886 Hom.: 5791 Cov.: 32 AF XY: 0.265 AC XY: 19704 AN XY: 74236

African (AFR) AF: 0.180 AC: 7452 AN: 41456

American (AMR) AF: 0.290 AC: 4424 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1383 AN: 5128

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2202 AN: 10552

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21125 AN: 67918

Other (OTH) AF: 0.299 AC: 630 AN: 2108

Alfa AF: 0.297 Hom.: 22159

Bravo AF: 0.269

Asia WGS AF: 0.228 AC: 791 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	4.4
DANN	Benign	0.89
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs9390939; hg19: chr6-103484412;