rs1362136

chr7-2465932-G-Achr7-2465932-G-C

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 0.388 in 152,052 control chromosomes in the GnomAD database, including 13,338 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 0.39 (13338 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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 = 0.77 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: 0.388 AC: 58925 AN: 151934 Hom.: 13335 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.388 AC: 58958 AN: 152052 Hom.: 13338 Cov.: 31 AF XY: 0.389 AC XY: 28931 AN XY: 74328

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.363

Alfa AF: 0.287 Hom.: 11330

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.1
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: rs1362136; hg19: chr7-2505567;