7-21123736-C-T

Variant names:

• chr7-21123736-C-T
• rs10950840

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 0.761 in 152,028 control chromosomes in the GnomAD database, including 44,093 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 0.76 (44093 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.761 AC: 115614 AN: 151910 Hom.: 44055 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.692

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.761 AC: 115707 AN: 152028 Hom.: 44093 Cov.: 31 AF XY: 0.763 AC XY: 56690 AN XY: 74318

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.750

Alfa AF: 0.746 Hom.: 70272

Bravo AF: 0.760

Asia WGS AF: 0.728 AC: 2535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10950840; hg19: chr7-21163355;