rs9471419

Variant names:

• chr6-40752964-T-C
• rs9471419

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 0.854 in 152,216 control chromosomes in the GnomAD database, including 55,934 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 0.85 (55934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.91 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: 0.855 AC: 130005 AN: 152098 Hom.: 55914 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.854 AC: 130067 AN: 152216 Hom.: 55934 Cov.: 31 AF XY: 0.859 AC XY: 63877 AN XY: 74400

African (AFR) AF: 0.757 AC: 31406 AN: 41496

American (AMR) AF: 0.847 AC: 12955 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3047 AN: 3470

East Asian (EAS) AF: 0.931 AC: 4820 AN: 5178

South Asian (SAS) AF: 0.933 AC: 4502 AN: 4824

European-Finnish (FIN) AF: 0.921 AC: 9765 AN: 10608

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60776 AN: 68032

Other (OTH) AF: 0.853 AC: 1802 AN: 2112

Alfa AF: 0.871 Hom.: 23334

Bravo AF: 0.842

Asia WGS AF: 0.892 AC: 3102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9471419; hg19: chr6-40720703; COSMIC: COSV56540768;