rs2876950

Variant names:

• chr7-51474665-C-T
• rs2876950
• ENST00000648455.1:n.193+2756C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648455.1(ENSG00000285741):​n.193+2756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,084 control chromosomes in the GnomAD database, including 975 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 0.097 (975 hom., cov: 32)
• Consequence: ENSG00000285741 ENST00000648455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 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
ENSG00000285741	ENST00000648455.1	n.193+2756C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14751 AN: 151968 Hom.: 972 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0800

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

GnomAD4 genome AF: 0.0971 AC: 14761 AN: 152084 Hom.: 975 Cov.: 32 AF XY: 0.104 AC XY: 7702 AN XY: 74314

Gnomad4 AFR AF: 0.0319

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.112 Hom.: 165

Bravo AF: 0.0825

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2876950; hg19: chr7-51542362;