rs9379874

Variant names:

• chr6-26440201-A-T
• rs9379874
• ENST00000707189.1:n.1000-112986A>T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-112986A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,092 control chromosomes in the GnomAD database, including 23,449 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 0.53 (23449 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 9 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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
ENSG00000291336	ENST00000707189.1	n.1000-112986A>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-92504A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79784 AN: 151974 Hom.: 23404 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.525 AC: 79880 AN: 152092 Hom.: 23449 Cov.: 32 AF XY: 0.521 AC XY: 38725 AN XY: 74356

African (AFR) AF: 0.805 AC: 33397 AN: 41504

American (AMR) AF: 0.441 AC: 6737 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1391 AN: 5188

South Asian (SAS) AF: 0.406 AC: 1958 AN: 4822

European-Finnish (FIN) AF: 0.471 AC: 4975 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28493 AN: 67962

Other (OTH) AF: 0.481 AC: 1015 AN: 2112

Alfa AF: 0.478 Hom.: 2504

Bravo AF: 0.539

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.57
PromoterAI		-0.038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9379874; hg19: chr6-26440429;