7-10796462-C-T

Variant names:

• chr7-10796462-C-T
• rs12673360

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.258 AC: 10681 AN: 41444

American (AMR) AF: 0.176 AC: 2686 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1111 AN: 3464

East Asian (EAS) AF: 0.380 AC: 1958 AN: 5158

South Asian (SAS) AF: 0.203 AC: 977 AN: 4802

European-Finnish (FIN) AF: 0.277 AC: 2932 AN: 10568

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17414 AN: 67964

Other (OTH) AF: 0.235 AC: 495 AN: 2108

Alfa AF: 0.247 Hom.: 10782

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12673360; hg19: chr7-10836089;