6-103351171-C-T

Variant names:

• chr6-103351171-C-T
• rs994988

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 0.448 in 151,548 control chromosomes in the GnomAD database, including 16,953 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 0.45 (16953 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 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: 0.449 AC: 67943 AN: 151428 Hom.: 16951 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.448 AC: 67956 AN: 151548 Hom.: 16953 Cov.: 30 AF XY: 0.455 AC XY: 33652 AN XY: 73994

African (AFR) AF: 0.216 AC: 8930 AN: 41336

American (AMR) AF: 0.524 AC: 7967 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1807 AN: 3464

East Asian (EAS) AF: 0.598 AC: 3056 AN: 5110

South Asian (SAS) AF: 0.619 AC: 2975 AN: 4808

European-Finnish (FIN) AF: 0.565 AC: 5900 AN: 10446

Middle Eastern (MID) AF: 0.469 AC: 134 AN: 286

European-Non Finnish (NFE) AF: 0.527 AC: 35783 AN: 67890

Other (OTH) AF: 0.443 AC: 926 AN: 2090

Alfa AF: 0.498 Hom.: 77029

Bravo AF: 0.431

Asia WGS AF: 0.562 AC: 1953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs994988; hg19: chr6-103799046;