rs4960575

Variant names:

• chr7-155054081-C-A
• rs4960575

Your query was ambiguous. Multiple possible variants found:

• chr7-155054081-C-A
• chr7-155054081-C-G
• chr7-155054081-C-T

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 0.502 in 152,018 control chromosomes in the GnomAD database, including 21,082 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 0.50 (21082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 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: 0.502 AC: 76229 AN: 151900 Hom.: 21080 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.502 AC: 76248 AN: 152018 Hom.: 21082 Cov.: 32 AF XY: 0.495 AC XY: 36806 AN XY: 74300

African (AFR) AF: 0.272 AC: 11295 AN: 41452

American (AMR) AF: 0.553 AC: 8452 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2171 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5162

South Asian (SAS) AF: 0.516 AC: 2480 AN: 4810

European-Finnish (FIN) AF: 0.520 AC: 5493 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43302 AN: 67970

Other (OTH) AF: 0.519 AC: 1097 AN: 2114

Alfa AF: 0.449 Hom.: 2023

Bravo AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.78
DANN	Benign	0.42
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4960575; hg19: chr7-154845791;