rs1404419

Variant names:

• chr7-17774405-C-T
• rs1404419

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 0.583 in 151,736 control chromosomes in the GnomAD database, including 26,167 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 (26167 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.583 AC: 88445 AN: 151618 Hom.: 26142 Cov.: 30

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.583 AC: 88521 AN: 151736 Hom.: 26167 Cov.: 30 AF XY: 0.584 AC XY: 43245 AN XY: 74100

African (AFR) AF: 0.615 AC: 25433 AN: 41356

American (AMR) AF: 0.667 AC: 10174 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4144 AN: 5094

South Asian (SAS) AF: 0.612 AC: 2942 AN: 4810

European-Finnish (FIN) AF: 0.504 AC: 5294 AN: 10508

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36563 AN: 67946

Other (OTH) AF: 0.581 AC: 1224 AN: 2108

Alfa AF: 0.560 Hom.: 3000

Bravo AF: 0.597

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.020
DANN	Benign	0.20
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1404419; hg19: chr7-17814029;