chr8-36601936-T-C

Variant names:

• chr8-36601936-T-C
• rs7814403
• ENST00000524132.6:n.530-64460A>G

Variant summary

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

The ENST00000524132.6(ENSG00000253363):​n.530-64460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,040 control chromosomes in the GnomAD database, including 15,355 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 0.45 (15355 hom., cov: 32)
• Consequence: ENSG00000253363 ENST00000524132.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 4 publications found

Genes affected

ENSG00000253363 (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 (NFE) allele frequency at 95% confidence interval = 0.475 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
ENSG00000253363	ENST00000524132.6	n.530-64460A>G		intron_variant	Intron 4 of 4	4
ENSG00000253363	ENST00000651399.1	n.516+99885A>G		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2	n.484+99885A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68159 AN: 151922 Hom.: 15330 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.449 AC: 68228 AN: 152040 Hom.: 15355 Cov.: 32 AF XY: 0.448 AC XY: 33305 AN XY: 74316

African (AFR) AF: 0.414 AC: 17171 AN: 41456

American (AMR) AF: 0.437 AC: 6672 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1417 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5158

South Asian (SAS) AF: 0.385 AC: 1859 AN: 4828

European-Finnish (FIN) AF: 0.458 AC: 4852 AN: 10588

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.479 AC: 32573 AN: 67968

Other (OTH) AF: 0.440 AC: 927 AN: 2108

Alfa AF: 0.463 Hom.: 59316

Bravo AF: 0.444

Asia WGS AF: 0.415 AC: 1443 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	0.95
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7814403; hg19: chr8-36459454;