rs9368677

Variant names:

• chr6-31304544-G-A
• rs9368677
• ENST00000755297.1:n.32+33438G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+33438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,200 control chromosomes in the GnomAD database, including 548 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 0.077 (548 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 29 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.964+2234C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+33438G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11679 AN: 152084 Hom.: 545 Cov.: 31

Gnomad AFR AF: 0.0651

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0769 AC: 11703 AN: 152200 Hom.: 548 Cov.: 31 AF XY: 0.0796 AC XY: 5922 AN XY: 74416

African (AFR) AF: 0.0653 AC: 2710 AN: 41530

American (AMR) AF: 0.0961 AC: 1469 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1102 AN: 5174

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4824

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10592

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0705 AC: 4793 AN: 68012

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0728 Hom.: 1337

Bravo AF: 0.0785

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.71
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs9368677; hg19: chr6-31272321;