rs1980057

Positions:

• chr4-144564586-C-T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-148608G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,034 control chromosomes in the GnomAD database, including 9,459 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 0.32 (9459 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144564586C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-148608G>A		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-148608G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48393 AN: 151916 Hom.: 9450 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.318 AC: 48405 AN: 152034 Hom.: 9459 Cov.: 32 AF XY: 0.326 AC XY: 24197 AN XY: 74320

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.304

Alfa AF: 0.386 Hom.: 22039

Bravo AF: 0.284

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1980057; hg19: chr4-145485738;