rs1980057

Variant names:

• chr4-144564586-C-T
• rs1980057
• ENST00000649263.1:n.328-148608G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 55 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-148608G>A		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-148608G>A		intron_variant	Intron 2 of 14

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

African (AFR) AF: 0.0945 AC: 3919 AN: 41488

American (AMR) AF: 0.303 AC: 4630 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3464

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5162

South Asian (SAS) AF: 0.492 AC: 2369 AN: 4816

European-Finnish (FIN) AF: 0.537 AC: 5668 AN: 10560

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27991 AN: 67956

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.380 Hom.: 46650

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1980057; hg19: chr4-145485738;