rs1476471

Variant names:

• chr7-109291458-C-G
• rs1476471

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 0.575 in 152,022 control chromosomes in the GnomAD database, including 26,645 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 0.58 (26645 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.575 AC: 87369 AN: 151904 Hom.: 26640 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.575 AC: 87416 AN: 152022 Hom.: 26645 Cov.: 33 AF XY: 0.590 AC XY: 43836 AN XY: 74286

African (AFR) AF: 0.416 AC: 17261 AN: 41448

American (AMR) AF: 0.673 AC: 10288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3464

East Asian (EAS) AF: 0.993 AC: 5149 AN: 5184

South Asian (SAS) AF: 0.736 AC: 3551 AN: 4824

European-Finnish (FIN) AF: 0.752 AC: 7949 AN: 10570

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39883 AN: 67934

Other (OTH) AF: 0.562 AC: 1187 AN: 2112

Alfa AF: 0.575 Hom.: 3166

Bravo AF: 0.560

Asia WGS AF: 0.818 AC: 2836 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.56
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1476471; hg19: chr7-108931515;