rs10271302

Variant names:

• chr7-27353755-C-T
• rs10271302

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 0.351 in 152,022 control chromosomes in the GnomAD database, including 10,874 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 0.35 (10874 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• 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 (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.352 AC: 53425 AN: 151904 Hom.: 10877 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.351 AC: 53426 AN: 152022 Hom.: 10874 Cov.: 32 AF XY: 0.350 AC XY: 25989 AN XY: 74280

African (AFR) AF: 0.144 AC: 5986 AN: 41478

American (AMR) AF: 0.370 AC: 5646 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1445 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1335 AN: 5158

South Asian (SAS) AF: 0.338 AC: 1632 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4691 AN: 10544

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31369 AN: 67960

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.421 Hom.: 26884

Bravo AF: 0.334

Asia WGS AF: 0.254 AC: 886 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	6.4
DANN	Benign	0.66
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10271302; hg19: chr7-27393374;