6-102838585-G-C

Variant names:

• chr6-102838585-G-C
• rs7769478

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 0.487 in 151,932 control chromosomes in the GnomAD database, including 18,571 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 0.49 (18571 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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: 0.487 AC: 73867 AN: 151814 Hom.: 18547 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.487 AC: 73957 AN: 151932 Hom.: 18571 Cov.: 31 AF XY: 0.480 AC XY: 35633 AN XY: 74252

African (AFR) AF: 0.575 AC: 23836 AN: 41420

American (AMR) AF: 0.408 AC: 6227 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.177 AC: 916 AN: 5164

South Asian (SAS) AF: 0.403 AC: 1938 AN: 4814

European-Finnish (FIN) AF: 0.502 AC: 5279 AN: 10518

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32644 AN: 67966

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.471 Hom.: 2110

Bravo AF: 0.481

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7769478; hg19: chr6-103286460;