ENST00000655001.1:n.386+9769G>A

Variant names:

• chr8-60084492-G-A
• rs997493
• ENST00000655001.1:n.386+9769G>A

Variant summary

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

The ENST00000655001.1(ENSG00000254775):​n.386+9769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,030 control chromosomes in the GnomAD database, including 3,583 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 0.20 (3583 hom., cov: 32)
• Consequence: ENSG00000254775 ENST00000655001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 2 publications found

Genes affected

ENSG00000254775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375861	XR_001745714.3	n.632+9769G>A		intron_variant	Intron 4 of 4
LOC105375861	XR_007060918.1	n.354+9769G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254775	ENST00000655001.1	n.386+9769G>A		intron_variant	Intron 3 of 3
ENSG00000254775	ENST00000655977.1	n.360+9769G>A		intron_variant	Intron 3 of 3
ENSG00000254775	ENST00000658208.1	n.354+9769G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30791 AN: 151910 Hom.: 3586 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.202 AC: 30781 AN: 152030 Hom.: 3583 Cov.: 32 AF XY: 0.204 AC XY: 15175 AN XY: 74318

African (AFR) AF: 0.102 AC: 4240 AN: 41406

American (AMR) AF: 0.171 AC: 2613 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5176

South Asian (SAS) AF: 0.296 AC: 1430 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2312 AN: 10578

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16875 AN: 67992

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.215 Hom.: 504

Bravo AF: 0.193

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs997493; hg19: chr8-60997051;