7-112603259-G-C

Position:

• chr7-112603259-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 0.478 in 151,698 control chromosomes in the GnomAD database, including 17,722 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 0.48 (17722 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72392 AN: 151582 Hom.: 17714 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.478 AC: 72451 AN: 151698 Hom.: 17722 Cov.: 31 AF XY: 0.473 AC XY: 35048 AN XY: 74146

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.461

Alfa AF: 0.381 Hom.: 1041

Bravo AF: 0.476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs43077; hg19: chr7-112243314;