rs10261327

Variant names:

• chr7-21423210-T-C
• rs10261327

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 0.538 in 151,910 control chromosomes in the GnomAD database, including 22,201 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 0.54 (22201 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 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: 0.538 AC: 81607 AN: 151794 Hom.: 22184 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.538 AC: 81671 AN: 151910 Hom.: 22201 Cov.: 31 AF XY: 0.533 AC XY: 39607 AN XY: 74252

African (AFR) AF: 0.553 AC: 22914 AN: 41404

American (AMR) AF: 0.450 AC: 6872 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1543 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2703 AN: 5162

South Asian (SAS) AF: 0.405 AC: 1954 AN: 4822

European-Finnish (FIN) AF: 0.606 AC: 6378 AN: 10530

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.554 AC: 37653 AN: 67946

Other (OTH) AF: 0.503 AC: 1061 AN: 2108

Alfa AF: 0.534 Hom.: 37061

Bravo AF: 0.527

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs10261327; hg19: chr7-21462828;