rs940031

Variant names:

• chr8-8689338-G-A
• rs940031
• ENST00000765578.1:n.660+34192C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-8689338-G-A
• chr8-8689338-G-C

Variant summary

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

The ENST00000765578.1(ENSG00000254367):​n.660+34192C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,066 control chromosomes in the GnomAD database, including 8,080 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 0.32 (8080 hom., cov: 33)
• Consequence: ENSG00000254367 ENST00000765578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 13 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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
ENSG00000254367	ENST00000765578.1	n.660+34192C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47971 AN: 151948 Hom.: 8078 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.316 AC: 47985 AN: 152066 Hom.: 8080 Cov.: 33 AF XY: 0.308 AC XY: 22861 AN XY: 74324

African (AFR) AF: 0.274 AC: 11352 AN: 41472

American (AMR) AF: 0.244 AC: 3726 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1491 AN: 3472

East Asian (EAS) AF: 0.0620 AC: 322 AN: 5192

South Asian (SAS) AF: 0.242 AC: 1162 AN: 4808

European-Finnish (FIN) AF: 0.284 AC: 3003 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25826 AN: 67978

Other (OTH) AF: 0.326 AC: 688 AN: 2112

Alfa AF: 0.344 Hom.: 7110

Bravo AF: 0.308

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs940031; hg19: chr8-8546848;