chr4-60157175-G-A

Variant names:

• chr4-60157175-G-A
• rs1441302

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 0.0637 in 151,966 control chromosomes in the GnomAD database, including 432 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 0.064 (432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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: 0.0636 AC: 9657 AN: 151848 Hom.: 425 Cov.: 31

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0637 AC: 9676 AN: 151966 Hom.: 432 Cov.: 31 AF XY: 0.0673 AC XY: 4997 AN XY: 74266

African (AFR) AF: 0.0334 AC: 1385 AN: 41454

American (AMR) AF: 0.0550 AC: 840 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1223 AN: 5120

South Asian (SAS) AF: 0.157 AC: 757 AN: 4822

European-Finnish (FIN) AF: 0.0741 AC: 781 AN: 10538

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0608 AC: 4135 AN: 67980

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0677 Hom.: 228

Bravo AF: 0.0601

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1441302; hg19: chr4-61022893;