chr7-35515178-C-T

Variant names:

• chr7-35515178-C-T
• rs343064

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 0.324 in 151,576 control chromosomes in the GnomAD database, including 9,169 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 0.32 (9169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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: 0.324 AC: 49126 AN: 151458 Hom.: 9156 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.324 AC: 49161 AN: 151576 Hom.: 9169 Cov.: 31 AF XY: 0.326 AC XY: 24117 AN XY: 74024

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.340

Alfa AF: 0.382 Hom.: 12615

Bravo AF: 0.319

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs343064; hg19: chr7-35554788;