10-44585946-T-A

Variant names:

• chr10-44585946-T-A
• rs1999774
• ENST00000738582.1:n.90+2991T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000738582.1(ENSG00000296361):​n.90+2991T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,012 control chromosomes in the GnomAD database, including 13,178 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 0.39 (13178 hom., cov: 32)
• Consequence: ENSG00000296361 ENST00000738582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 3 publications found

Genes affected

ENSG00000296361 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738582.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296361	ENST00000738582.1		n.90+2991T>A		intron	N/A
	ENSG00000296361	ENST00000738583.1		n.90+2991T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58966 AN: 151894 Hom.: 13164 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.388 AC: 59015 AN: 152012 Hom.: 13178 Cov.: 32 AF XY: 0.392 AC XY: 29159 AN XY: 74296

African (AFR) AF: 0.154 AC: 6408 AN: 41480

American (AMR) AF: 0.483 AC: 7375 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2295 AN: 5154

South Asian (SAS) AF: 0.511 AC: 2456 AN: 4810

European-Finnish (FIN) AF: 0.503 AC: 5293 AN: 10532

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32363 AN: 67976

Other (OTH) AF: 0.411 AC: 866 AN: 2108

Alfa AF: 0.301 Hom.: 859

Bravo AF: 0.379

Asia WGS AF: 0.485 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.80
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1999774; hg19: chr10-45081394;