rs36061340

Variant names:

• chr8-100795002-C-T
• rs36061340
• ENST00000822257.1:n.89-772C>T

Variant summary

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

The ENST00000822257.1(ENSG00000306968):​n.89-772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,572 control chromosomes in the GnomAD database, including 1,204 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 0.11 (1204 hom., cov: 29)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 5 publications found

Genes affected

ENSG00000306968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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
ENSG00000306968	ENST00000822257.1	n.89-772C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16288 AN: 151456 Hom.: 1195 Cov.: 29

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.108 AC: 16335 AN: 151572 Hom.: 1204 Cov.: 29 AF XY: 0.111 AC XY: 8248 AN XY: 74088

African (AFR) AF: 0.151 AC: 6245 AN: 41224

American (AMR) AF: 0.196 AC: 2979 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1624 AN: 5110

South Asian (SAS) AF: 0.0832 AC: 400 AN: 4806

European-Finnish (FIN) AF: 0.0560 AC: 590 AN: 10544

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0577 AC: 3917 AN: 67884

Other (OTH) AF: 0.114 AC: 240 AN: 2104

Alfa AF: 0.0857 Hom.: 84

Bravo AF: 0.123

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.43
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs36061340; hg19: chr8-101807230;