rs1586149

Variant names:

• chr4-126153633-C-A
• rs1586149

Your query was ambiguous. Multiple possible variants found:

• chr4-126153633-C-A
• chr4-126153633-C-G
• chr4-126153633-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 0.096 in 151,908 control chromosomes in the GnomAD database, including 1,456 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 0.096 (1456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.0960 AC: 14565 AN: 151790 Hom.: 1447 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0832

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.0960 AC: 14589 AN: 151908 Hom.: 1456 Cov.: 32 AF XY: 0.102 AC XY: 7585 AN XY: 74260

African (AFR) AF: 0.0626 AC: 2584 AN: 41300

American (AMR) AF: 0.160 AC: 2442 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2832 AN: 5160

South Asian (SAS) AF: 0.206 AC: 994 AN: 4828

European-Finnish (FIN) AF: 0.0832 AC: 882 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4458 AN: 67964

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0826 Hom.: 150

Bravo AF: 0.101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1586149; hg19: chr4-127074788;