rs6474491

Variant names:

• chr8-38156330-T-C
• rs6474491
• ENST00000520598.1:n.100-6980T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-38156330-T-C
• chr8-38156330-T-G

Variant summary

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

The ENST00000520598.1(ENSG00000253356):​n.100-6980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,010 control chromosomes in the GnomAD database, including 4,759 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 0.25 (4759 hom., cov: 31)
• Consequence: ENSG00000253356 ENST00000520598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 11 publications found

Genes affected

ENSG00000253356 (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 (SAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520598.1. 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
	ENSG00000253356	ENST00000520598.1	TSL:4	n.100-6980T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37395 AN: 151890 Hom.: 4761 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.246 AC: 37419 AN: 152010 Hom.: 4759 Cov.: 31 AF XY: 0.247 AC XY: 18362 AN XY: 74286

African (AFR) AF: 0.233 AC: 9648 AN: 41430

American (AMR) AF: 0.218 AC: 3328 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1716 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4818

European-Finnish (FIN) AF: 0.208 AC: 2200 AN: 10574

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16818 AN: 67980

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.252 Hom.: 10550

Bravo AF: 0.243

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		0.16

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: rs6474491;

hg19: chr8-38013848;