rs2007960

Variant names:

• chr14-35413729-A-T
• rs2007960

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 0.624 in 152,084 control chromosomes in the GnomAD database, including 29,840 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 0.62 (29840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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: 0.624 AC: 94837 AN: 151966 Hom.: 29798 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.624 AC: 94930 AN: 152084 Hom.: 29840 Cov.: 32 AF XY: 0.630 AC XY: 46819 AN XY: 74356

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.615

Alfa AF: 0.621 Hom.: 3654

Bravo AF: 0.625

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2007960; hg19: chr14-35882935;