rs7662987

Variant names:

• chr4-99070491-T-C
• rs7662987

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 0.0841 in 152,296 control chromosomes in the GnomAD database, including 576 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 0.084 (576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0983 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: 0.0841 AC: 12805 AN: 152178 Hom.: 576 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.0841 AC: 12813 AN: 152296 Hom.: 576 Cov.: 32 AF XY: 0.0792 AC XY: 5901 AN XY: 74466

African (AFR) AF: 0.0831 AC: 3453 AN: 41570

American (AMR) AF: 0.0856 AC: 1310 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0349 AC: 168 AN: 4818

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6822 AN: 68022

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.101 Hom.: 802

Bravo AF: 0.0880

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.61
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7662987; hg19: chr4-99991642;