6-111620953-T-C

Variant names:

• chr6-111620953-T-C
• rs7748820

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 0.624 in 152,026 control chromosomes in the GnomAD database, including 29,931 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 0.62 (29931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94835 AN: 151908 Hom.: 29923 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.624 AC: 94892 AN: 152026 Hom.: 29931 Cov.: 32 AF XY: 0.624 AC XY: 46381 AN XY: 74302

African (AFR) AF: 0.562 AC: 23306 AN: 41458

American (AMR) AF: 0.684 AC: 10446 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2593 AN: 5152

South Asian (SAS) AF: 0.591 AC: 2845 AN: 4812

European-Finnish (FIN) AF: 0.617 AC: 6518 AN: 10562

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45010 AN: 67986

Other (OTH) AF: 0.655 AC: 1381 AN: 2108

Alfa AF: 0.647 Hom.: 26728

Bravo AF: 0.628

Asia WGS AF: 0.598 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0050
DANN	Benign	0.27
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7748820; hg19: chr6-111942156;