rs7662987

Positions:

• chr4-99070491-T-C

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 0.0841 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0349

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.102 Hom.: 707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7662987; hg19: chr4-99991642;