rs951629

Positions:

• chr2-9656662-G-A
• chr2-9656662-G-C

Variant summary

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

The ENST00000667551.1(ENSG00000240687):​n.471+15205G>A 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 0.542 in 152,056 control chromosomes in the GnomAD database, including 24,936 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 (24936 hom., cov: 32)
• Consequence: ENST00000667551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667551.1	n.471+15205G>A		intron_variant, non_coding_transcript_variant
	ENST00000663514.1	n.223+15205G>A		intron_variant, non_coding_transcript_variant
	ENST00000669600.1	n.413+7659G>A		intron_variant, non_coding_transcript_variant
	ENST00000702480.1	n.607+7659G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82381 AN: 151938 Hom.: 24891 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.542 AC: 82475 AN: 152056 Hom.: 24936 Cov.: 32 AF XY: 0.538 AC XY: 39948 AN XY: 74316

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.522

Alfa AF: 0.450 Hom.: 22650

Bravo AF: 0.549

Asia WGS AF: 0.427 AC: 1487 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	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951629; hg19: chr2-9796791; COSMIC: COSV69023118;