rs10261327

Positions:

• chr7-21423210-T-C

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 0.538 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.503

Alfa AF: 0.533 Hom.: 29351

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10261327; hg19: chr7-21462828;