rs7654585

Positions:

• chr4-25941129-A-G

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 0.594 in 152,044 control chromosomes in the GnomAD database, including 26,862 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 0.59 (26862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90218 AN: 151926 Hom.: 26843 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.594 AC: 90283 AN: 152044 Hom.: 26862 Cov.: 32 AF XY: 0.592 AC XY: 43969 AN XY: 74330

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.579

Alfa AF: 0.597 Hom.: 54166

Bravo AF: 0.596

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7654585; hg19: chr4-25942751;