rs491112

Variant names:

• chr6-93459929-C-A
• rs491112
• ENST00000668367.1:n.151+42828C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-93459929-C-A
• chr6-93459929-C-G
• chr6-93459929-C-T

Variant summary

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

The ENST00000668367.1(ENSG00000287683):​n.151+42828C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,926 control chromosomes in the GnomAD database, including 26,986 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 0.58 (26986 hom., cov: 32)
• Consequence: ENSG00000287683 ENST00000668367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 4 publications found

Genes affected

ENSG00000287683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668367.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287683	ENST00000668367.1		n.151+42828C>A		intron	N/A
	ENSG00000287683	ENST00000776530.1		n.169+42828C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87511 AN: 151808 Hom.: 26934 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.577 AC: 87628 AN: 151926 Hom.: 26986 Cov.: 32 AF XY: 0.582 AC XY: 43242 AN XY: 74256

African (AFR) AF: 0.793 AC: 32885 AN: 41468

American (AMR) AF: 0.599 AC: 9145 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3453 AN: 5158

South Asian (SAS) AF: 0.511 AC: 2455 AN: 4802

European-Finnish (FIN) AF: 0.576 AC: 6076 AN: 10540

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31089 AN: 67928

Other (OTH) AF: 0.513 AC: 1077 AN: 2100

Alfa AF: 0.479 Hom.: 2577

Bravo AF: 0.589

Asia WGS AF: 0.596 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.31
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs491112; hg19: chr6-94169647;