6-31417112-C-G

Variant names:

• chr6-31417112-C-G
• rs9266846
• ENST00000673857.1:n.62+16349C>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+16349C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,746 control chromosomes in the GnomAD database, including 7,691 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 0.31 (7691 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 7 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288587	ENST00000673857.1		n.62+16349C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46618 AN: 151626 Hom.: 7673 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.308 AC: 46686 AN: 151746 Hom.: 7691 Cov.: 32 AF XY: 0.314 AC XY: 23318 AN XY: 74168

African (AFR) AF: 0.359 AC: 14815 AN: 41272

American (AMR) AF: 0.336 AC: 5104 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1637 AN: 5170

South Asian (SAS) AF: 0.304 AC: 1462 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10570

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17415 AN: 67952

Other (OTH) AF: 0.300 AC: 634 AN: 2110

Alfa AF: 0.285 Hom.: 867

Bravo AF: 0.306

Asia WGS AF: 0.359 AC: 1245 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		0.028

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9266846;

hg19: chr6-31384889;