ENST00000762170.1:n.151+2960T>C

Variant names:

• chr6-95769047-T-C
• rs1361900
• ENST00000762170.1:n.151+2960T>C

Variant summary

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

The ENST00000762170.1(ENSG00000299276):​n.151+2960T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,282 control chromosomes in the GnomAD database, including 63,854 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 0.91 (63854 hom., cov: 33)
• Consequence: ENSG00000299276 ENST00000762170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 1 publications found

Genes affected

ENSG00000299276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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
ENSG00000299276	ENST00000762170.1	n.151+2960T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139226 AN: 152164 Hom.: 63814 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.915 AC: 139323 AN: 152282 Hom.: 63854 Cov.: 33 AF XY: 0.913 AC XY: 67949 AN XY: 74450

African (AFR) AF: 0.878 AC: 36489 AN: 41546

American (AMR) AF: 0.910 AC: 13915 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 3233 AN: 3472

East Asian (EAS) AF: 0.784 AC: 4060 AN: 5180

South Asian (SAS) AF: 0.885 AC: 4272 AN: 4828

European-Finnish (FIN) AF: 0.922 AC: 9774 AN: 10602

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64434 AN: 68034

Other (OTH) AF: 0.922 AC: 1950 AN: 2116

Alfa AF: 0.932 Hom.: 3622

Bravo AF: 0.914

Asia WGS AF: 0.841 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1361900; hg19: chr6-96216923;