chr7-10796462-C-T

Position:

• chr7-10796462-C-T

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 0.254 in 152,002 control chromosomes in the GnomAD database, including 5,046 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 0.25 (5046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.254 AC: 38558 AN: 151884 Hom.: 5045 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.254 AC: 38571 AN: 152002 Hom.: 5046 Cov.: 32 AF XY: 0.256 AC XY: 19045 AN XY: 74320

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.235

Alfa AF: 0.245 Hom.: 5743

Bravo AF: 0.247

Asia WGS AF: 0.269 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12673360; hg19: chr7-10836089;