rs7657356

chr4-73724067-C-T

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 0.0739 in 152,114 control chromosomes in the GnomAD database, including 666 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 0.074 (666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 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: 0.0739 AC: 11239 AN: 151996 Hom.: 667 Cov.: 32

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0739 AC: 11236 AN: 152114 Hom.: 666 Cov.: 32 AF XY: 0.0759 AC XY: 5646 AN XY: 74356

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.0539

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0351

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.0643 Hom.: 380

Bravo AF: 0.0759

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7657356; hg19: chr4-74589784;