rs1547625

Variant names:

• chr6-56440467-A-G
• rs1547625

Your query was ambiguous. Multiple possible variants found:

• chr6-56440467-A-G
• chr6-56440467-A-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 0.439 in 152,036 control chromosomes in the GnomAD database, including 16,173 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 0.44 (16173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.439 AC: 66708 AN: 151916 Hom.: 16146 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.439 AC: 66779 AN: 152036 Hom.: 16173 Cov.: 32 AF XY: 0.432 AC XY: 32129 AN XY: 74322

African (AFR) AF: 0.650 AC: 26931 AN: 41452

American (AMR) AF: 0.391 AC: 5967 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1395 AN: 5172

South Asian (SAS) AF: 0.413 AC: 1993 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2594 AN: 10584

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24628 AN: 67958

Other (OTH) AF: 0.456 AC: 962 AN: 2108

Alfa AF: 0.447 Hom.: 5850

Bravo AF: 0.458

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1547625; hg19: chr6-56305265;