rs1364616

Variant names:

• chr8-71654009-C-A
• rs1364616
• ENST00000723932.1:n.1196-5508G>T

Variant summary

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

The ENST00000723932.1(ENSG00000294494):​n.1196-5508G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,916 control chromosomes in the GnomAD database, including 12,560 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 0.39 (12560 hom., cov: 31)
• Consequence: ENSG00000294494 ENST00000723932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 4 publications found

Genes affected

ENSG00000294494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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
ENSG00000294494	ENST00000723932.1	n.1196-5508G>T		intron_variant	Intron 2 of 2
ENSG00000294494	ENST00000723933.1	n.212-5508G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58552 AN: 151798 Hom.: 12561 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.386 AC: 58574 AN: 151916 Hom.: 12560 Cov.: 31 AF XY: 0.383 AC XY: 28462 AN XY: 74240

African (AFR) AF: 0.203 AC: 8429 AN: 41444

American (AMR) AF: 0.378 AC: 5769 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1167 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2721 AN: 5168

South Asian (SAS) AF: 0.252 AC: 1217 AN: 4824

European-Finnish (FIN) AF: 0.496 AC: 5230 AN: 10544

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32676 AN: 67906

Other (OTH) AF: 0.340 AC: 715 AN: 2104

Alfa AF: 0.433 Hom.: 25113

Bravo AF: 0.371

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.6
DANN	Benign	0.82
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1364616; hg19: chr8-72566244;