rs7654585

Variant names:

• chr4-25941129-A-G
• rs7654585

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;