rs711513

Variant names:

• chr7-109728712-A-G
• rs711513

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 0.347 in 151,866 control chromosomes in the GnomAD database, including 9,349 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 0.35 (9349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.347 AC: 52622 AN: 151746 Hom.: 9340 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.347 AC: 52665 AN: 151866 Hom.: 9349 Cov.: 32 AF XY: 0.345 AC XY: 25591 AN XY: 74192

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.345

Alfa AF: 0.351 Hom.: 17647

Bravo AF: 0.333

Asia WGS AF: 0.293 AC: 1015 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs711513; hg19: chr7-109368769;