rs4960675

Variant names:

• chr7-155048924-G-A
• rs4960675

Your query was ambiguous. Multiple possible variants found:

• chr7-155048924-G-A
• chr7-155048924-G-C

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 0.232 in 152,148 control chromosomes in the GnomAD database, including 5,110 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 0.23 (5110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35292 AN: 152030 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.232 AC: 35306 AN: 152148 Hom.: 5110 Cov.: 32 AF XY: 0.236 AC XY: 17526 AN XY: 74370

African (AFR) AF: 0.0593 AC: 2462 AN: 41536

American (AMR) AF: 0.221 AC: 3376 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1115 AN: 5176

South Asian (SAS) AF: 0.310 AC: 1490 AN: 4808

European-Finnish (FIN) AF: 0.378 AC: 3993 AN: 10564

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21003 AN: 67986

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.174 Hom.: 457

Bravo AF: 0.212

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs4960675; hg19: chr7-154840634;