ENST00000730378.1:n.279+2444T>C

Variant names:

• chr10-119690755-A-G
• rs196241
• ENST00000730378.1:n.279+2444T>C

Variant summary

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

The ENST00000730378.1(ENSG00000295480):​n.279+2444T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,670 control chromosomes in the GnomAD database, including 29,385 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 0.62 (29385 hom., cov: 29)
• Consequence: ENSG00000295480 ENST00000730378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

ENSG00000295480 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730378.1. 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
	ENSG00000295480	ENST00000730378.1		n.279+2444T>C		intron	N/A
	ENSG00000295480	ENST00000730379.1		n.279+2444T>C		intron	N/A
	ENSG00000295480	ENST00000730380.1		n.228+2444T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93989 AN: 151550 Hom.: 29368 Cov.: 29

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.620 AC: 94041 AN: 151670 Hom.: 29385 Cov.: 29 AF XY: 0.619 AC XY: 45874 AN XY: 74118

African (AFR) AF: 0.582 AC: 24072 AN: 41332

American (AMR) AF: 0.754 AC: 11495 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3964 AN: 5152

South Asian (SAS) AF: 0.640 AC: 3078 AN: 4808

European-Finnish (FIN) AF: 0.528 AC: 5530 AN: 10480

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41761 AN: 67860

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.629 Hom.: 9869

Bravo AF: 0.636

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.93
DANN	Benign	0.080
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs196241; hg19: chr10-121450267;