rs2815752

Positions:

• chr1-72346757-G-A
• chr1-72346757-G-C

Variant summary

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

The ENST00000665984.1(ENSG00000286863):​n.153+63352G>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 0.625 in 151,932 control chromosomes in the GnomAD database, including 30,302 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 (30302 hom., cov: 31)
• Consequence: ENST00000665984.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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 (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.472+63352G>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_001737671.3	n.472+63352G>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947505.3	n.472+63352G>A		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947506.3	n.472+63352G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665984.1	n.153+63352G>A		intron_variant, non_coding_transcript_variant
	ENST00000653965.1	n.236+63352G>A		intron_variant, non_coding_transcript_variant
	ENST00000667836.1	n.227+63352G>A		intron_variant, non_coding_transcript_variant
	ENST00000688733.1	n.56+63352G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94889 AN: 151814 Hom.: 30286 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.625 AC: 94939 AN: 151932 Hom.: 30302 Cov.: 31 AF XY: 0.631 AC XY: 46861 AN XY: 74240

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.642

Alfa AF: 0.643 Hom.: 64560

Bravo AF: 0.628

Asia WGS AF: 0.753 AC: 2614 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2815752; hg19: chr1-72812440;