7-17774461-A-T

Variant names:

• chr7-17774461-A-T
• rs1404418

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 0.587 in 151,464 control chromosomes in the GnomAD database, including 26,449 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 0.59 (26449 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: 0.587 AC: 88842 AN: 151346 Hom.: 26425 Cov.: 29

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.587 AC: 88916 AN: 151464 Hom.: 26449 Cov.: 29 AF XY: 0.587 AC XY: 43401 AN XY: 73940

African (AFR) AF: 0.628 AC: 25890 AN: 41248

American (AMR) AF: 0.669 AC: 10183 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2182 AN: 3466

East Asian (EAS) AF: 0.814 AC: 4119 AN: 5062

South Asian (SAS) AF: 0.612 AC: 2932 AN: 4792

European-Finnish (FIN) AF: 0.505 AC: 5272 AN: 10446

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36547 AN: 67920

Other (OTH) AF: 0.582 AC: 1225 AN: 2104

Alfa AF: 0.555 Hom.: 2828

Bravo AF: 0.602

Asia WGS AF: 0.733 AC: 2547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1404418; hg19: chr7-17814085;