7-112603259-G-C

Variant names:

• chr7-112603259-G-C
• rs43077

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;