6-31302341-C-A

Variant names:

• chr6-31302341-C-A
• rs9468937
• ENST00000755297.1:n.32+31235C>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+31235C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,002 control chromosomes in the GnomAD database, including 20,576 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 0.51 (20576 hom., cov: 29)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 11 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.965-487G>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+31235C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77264 AN: 150884 Hom.: 20559 Cov.: 29

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.512 AC: 77323 AN: 151002 Hom.: 20576 Cov.: 29 AF XY: 0.516 AC XY: 38100 AN XY: 73774

African (AFR) AF: 0.623 AC: 25600 AN: 41098

American (AMR) AF: 0.477 AC: 7230 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2297 AN: 3460

East Asian (EAS) AF: 0.439 AC: 2247 AN: 5118

South Asian (SAS) AF: 0.604 AC: 2889 AN: 4782

European-Finnish (FIN) AF: 0.498 AC: 5195 AN: 10436

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30078 AN: 67652

Other (OTH) AF: 0.535 AC: 1121 AN: 2094

Alfa AF: 0.368 Hom.: 1304

Bravo AF: 0.513

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.20
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs9468937; hg19: chr6-31270118;