rs2876950

Positions:

• chr7-51474665-C-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, non coding transcript 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: ENST00000648455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648455.1	n.193+2756C>T		intron_variant, non_coding_transcript_variant

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;