rs2370025

Positions:

• chr1-192922893-G-A

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.104+2719C>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 0.436 in 151,986 control chromosomes in the GnomAD database, including 14,611 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 0.44 (14611 hom., cov: 33)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 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
	ENST00000644134.1	n.104+2719C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66212 AN: 151870 Hom.: 14588 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.436 AC: 66276 AN: 151986 Hom.: 14611 Cov.: 33 AF XY: 0.440 AC XY: 32683 AN XY: 74276

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.425

Alfa AF: 0.397 Hom.: 1543

Bravo AF: 0.432

Asia WGS AF: 0.560 AC: 1939 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2370025; hg19: chr1-192892023;