rs2816312

Positions:

• chr1-192581066-A-G
• chr1-192581066-A-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.468-11762T>C 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 0.136 in 151,990 control chromosomes in the GnomAD database, including 2,096 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 0.14 (2096 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371664	XR_002958418.2	n.287+12533T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.468-11762T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20605 AN: 151872 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.136 AC: 20633 AN: 151990 Hom.: 2096 Cov.: 32 AF XY: 0.132 AC XY: 9815 AN XY: 74296

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.0814

Gnomad4 ASJ AF: 0.0468

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0807

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.0782 Hom.: 175

Bravo AF: 0.143

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.38
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2816312; hg19: chr1-192550196;