7-81609395-A-T

Variant names:

• chr7-81609395-A-T
• rs17155256
• ENST00000413944.3:n.225-1752T>A

Variant summary

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

The ENST00000413944.3(ENSG00000293394):​n.225-1752T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0868 in 152,122 control chromosomes in the GnomAD database, including 1,339 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 0.087 (1339 hom., cov: 32)
• Consequence: ENSG00000293394 ENST00000413944.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 1 publications found

Genes affected

ENSG00000293394 (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 (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128317	NR_126025.1	n.225-1752T>A		intron_variant	Intron 3 of 10
LOC100128317	NR_126026.1	n.179-1752T>A		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293394	ENST00000413944.3	n.225-1752T>A		intron_variant	Intron 3 of 10	1
ENSG00000293394	ENST00000455420.5	n.179-1752T>A		intron_variant	Intron 2 of 8	1
ENSG00000293394	ENST00000636281.1	n.229-1752T>A		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13156 AN: 152006 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0196

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0868 AC: 13197 AN: 152122 Hom.: 1339 Cov.: 32 AF XY: 0.0907 AC XY: 6744 AN XY: 74366

African (AFR) AF: 0.197 AC: 8163 AN: 41522

American (AMR) AF: 0.0533 AC: 814 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5152

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4824

European-Finnish (FIN) AF: 0.0196 AC: 208 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 837 AN: 67944

Other (OTH) AF: 0.0773 AC: 163 AN: 2108

Alfa AF: 0.0423 Hom.: 63

Bravo AF: 0.0918

Asia WGS AF: 0.309 AC: 1072 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	4.7
DANN	Benign	0.67
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs17155256; hg19: chr7-81238711;