rs4075546

Variant names:

• chr15-66791903-A-G
• rs4075546

Your query was ambiguous. Multiple possible variants found:

• chr15-66791903-A-G
• chr15-66791903-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 0.346 in 151,988 control chromosomes in the GnomAD database, including 9,226 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 0.35 (9226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.384 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: 0.345 AC: 52462 AN: 151872 Hom.: 9209 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.346 AC: 52515 AN: 151988 Hom.: 9226 Cov.: 31 AF XY: 0.340 AC XY: 25254 AN XY: 74290

African (AFR) AF: 0.325 AC: 13457 AN: 41420

American (AMR) AF: 0.279 AC: 4261 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.157 AC: 813 AN: 5180

South Asian (SAS) AF: 0.327 AC: 1569 AN: 4796

European-Finnish (FIN) AF: 0.347 AC: 3673 AN: 10570

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26329 AN: 67950

Other (OTH) AF: 0.334 AC: 705 AN: 2110

Alfa AF: 0.371 Hom.: 5543

Bravo AF: 0.334

Asia WGS AF: 0.259 AC: 909 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	3.5
DANN	Benign	0.56
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs4075546; hg19: chr15-67084241;