ENST00000762194.1:n.377+961A>T

Variant names:

• chr4-99401872-T-A
• rs284794
• ENST00000762194.1:n.377+961A>T

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.377+961A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 152,208 control chromosomes in the GnomAD database, including 719 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 0.094 (719 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 3 publications found

Genes affected

ENSG00000299279 (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 (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.387+961A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1284+961A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1284+961A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.377+961A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762195.1	n.249+961A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762196.1	n.492+961A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762197.1	n.249+961A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14315 AN: 152090 Hom.: 714 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0942 AC: 14341 AN: 152208 Hom.: 719 Cov.: 32 AF XY: 0.0915 AC XY: 6812 AN XY: 74414

African (AFR) AF: 0.119 AC: 4944 AN: 41522

American (AMR) AF: 0.0777 AC: 1188 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0322 AC: 155 AN: 4814

European-Finnish (FIN) AF: 0.106 AC: 1121 AN: 10606

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0900 AC: 6120 AN: 68012

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.0935 Hom.: 85

Bravo AF: 0.0938

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.89
DANN	Benign	0.47
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs284794; hg19: chr4-100323029;