rs1404419

chr7-17774405-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.581

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404419; hg19: chr7-17814029;