chr7-99995723-C-A

Variant names:

• chr7-99995723-C-A
• rs4727443

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 0.346 in 151,912 control chromosomes in the GnomAD database, including 10,474 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 0.35 (10474 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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: 0.346 AC: 52535 AN: 151794 Hom.: 10470 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.346 AC: 52555 AN: 151912 Hom.: 10474 Cov.: 31 AF XY: 0.352 AC XY: 26110 AN XY: 74276

African (AFR) AF: 0.160 AC: 6635 AN: 41448

American (AMR) AF: 0.473 AC: 7213 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3466

East Asian (EAS) AF: 0.644 AC: 3320 AN: 5158

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4814

European-Finnish (FIN) AF: 0.345 AC: 3651 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26746 AN: 67894

Other (OTH) AF: 0.391 AC: 823 AN: 2106

Alfa AF: 0.383 Hom.: 51301

Bravo AF: 0.350

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4727443; hg19: chr7-99593346;