6-111620953-T-C

Variant names:

• chr6-111620953-T-C
• rs7748820

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.624 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

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.655

Alfa AF: 0.642 Hom.: 16588

Bravo AF: 0.628

Asia WGS AF: 0.598 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7748820; hg19: chr6-111942156;