chr6-104215903-G-C

Variant names:

• chr6-104215903-G-C
• rs2744203

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 0.125 in 151,934 control chromosomes in the GnomAD database, including 1,290 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 0.13 (1290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.125 AC: 19008 AN: 151816 Hom.: 1287 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.125 AC: 19016 AN: 151934 Hom.: 1290 Cov.: 32 AF XY: 0.121 AC XY: 8955 AN XY: 74228

African (AFR) AF: 0.178 AC: 7382 AN: 41438

American (AMR) AF: 0.0990 AC: 1510 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.0827 AC: 427 AN: 5164

South Asian (SAS) AF: 0.0476 AC: 229 AN: 4812

European-Finnish (FIN) AF: 0.0859 AC: 905 AN: 10534

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7557 AN: 67952

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.0430 Hom.: 42

Bravo AF: 0.131

Asia WGS AF: 0.0590 AC: 206 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.75
DANN	Benign	0.69
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2744203; hg19: chr6-104663778; COSMIC: COSV69418434;