7-54715680-T-C

Variant names:

• chr7-54715680-T-C
• rs6946131

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 0.436 in 152,108 control chromosomes in the GnomAD database, including 14,737 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 0.44 (14737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 9 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 (SAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66261 AN: 151990 Hom.: 14713 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.436 AC: 66337 AN: 152108 Hom.: 14737 Cov.: 32 AF XY: 0.433 AC XY: 32208 AN XY: 74376

African (AFR) AF: 0.477 AC: 19775 AN: 41476

American (AMR) AF: 0.381 AC: 5823 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1823 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1304 AN: 5178

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4297 AN: 10598

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29389 AN: 67964

Other (OTH) AF: 0.462 AC: 975 AN: 2110

Alfa AF: 0.419 Hom.: 6635

Bravo AF: 0.434

Asia WGS AF: 0.389 AC: 1355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6946131; hg19: chr7-54783373;