6-31309310-G-A

Variant names:

• chr6-31309310-G-A
• rs1634789
• ENST00000755297.1:n.32+38204G>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+38204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 147,578 control chromosomes in the GnomAD database, including 36,356 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 0.67 (36356 hom., cov: 30)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.782 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
ENSG00000298396	ENST00000755297.1	n.32+38204G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 98403 AN: 147470 Hom.: 36309 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.667 AC: 98503 AN: 147578 Hom.: 36356 Cov.: 30 AF XY: 0.673 AC XY: 48333 AN XY: 71832

African (AFR) AF: 0.764 AC: 30814 AN: 40324

American (AMR) AF: 0.794 AC: 11686 AN: 14726

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3037 AN: 3418

East Asian (EAS) AF: 0.689 AC: 2941 AN: 4270

South Asian (SAS) AF: 0.717 AC: 3255 AN: 4540

European-Finnish (FIN) AF: 0.578 AC: 5920 AN: 10234

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 38405 AN: 66848

Other (OTH) AF: 0.767 AC: 1552 AN: 2024

Alfa AF: 0.667 Hom.: 11349

Asia WGS AF: 0.719 AC: 2330 AN: 3240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.14
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1634789; hg19: chr6-31277087;