6-31368124-A-G

Variant names:

• chr6-31368124-A-G
• rs2922994
• ENST00000649421.2:n.274+794A>G

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.274+794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.089 in 133,722 control chromosomes in the GnomAD database, including 627 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 0.089 (627 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 26 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285647	ENST00000649421.2		n.274+794A>G		intron	N/A
	ENSG00000298426	ENST00000755446.1		n.327-13856A>G		intron	N/A
	ENSG00000285647	ENST00000755530.1		n.203-6759A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 11896 AN: 133620 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.0447

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.00594

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.0476

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0890 AC: 11900 AN: 133722 Hom.: 627 Cov.: 32 AF XY: 0.0845 AC XY: 5497 AN XY: 65076

African (AFR) AF: 0.0447 AC: 1535 AN: 34366

American (AMR) AF: 0.0449 AC: 594 AN: 13218

Ashkenazi Jewish (ASJ) AF: 0.0504 AC: 159 AN: 3154

East Asian (EAS) AF: 0.00573 AC: 24 AN: 4192

South Asian (SAS) AF: 0.0807 AC: 302 AN: 3744

European-Finnish (FIN) AF: 0.0909 AC: 910 AN: 10008

Middle Eastern (MID) AF: 0.0466 AC: 11 AN: 236

European-Non Finnish (NFE) AF: 0.130 AC: 8098 AN: 62164

Other (OTH) AF: 0.0727 AC: 129 AN: 1774

Alfa AF: 0.0677 Hom.: 168

Bravo AF: 0.0720

Asia WGS AF: 0.0230 AC: 77 AN: 3280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2922994; hg19: chr6-31335901;