7-17774053-C-T

Variant names:

• chr7-17774053-C-T
• rs2723520

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 0.585 in 151,994 control chromosomes in the GnomAD database, including 26,387 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 (26387 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.585 AC: 88855 AN: 151876 Hom.: 26362 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.586

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: 0.585 AC: 88931 AN: 151994 Hom.: 26387 Cov.: 31 AF XY: 0.585 AC XY: 43465 AN XY: 74298

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.581

Alfa AF: 0.555 Hom.: 47246

Bravo AF: 0.599

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0030
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2723520; hg19: chr7-17813677;