chr7-10279141-T-C

Variant names:

• chr7-10279141-T-C
• rs10224072

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 0.792 in 151,888 control chromosomes in the GnomAD database, including 47,943 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 0.79 (47943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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 (AFR) allele frequency at 95% confidence interval = 0.883 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: 0.791 AC: 120126 AN: 151770 Hom.: 47891 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.792 AC: 120238 AN: 151888 Hom.: 47943 Cov.: 31 AF XY: 0.786 AC XY: 58370 AN XY: 74216

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.782

Alfa AF: 0.755 Hom.: 54074

Bravo AF: 0.798

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10224072; hg19: chr7-10318768;