6-6331703-T-C

Variant names:

• chr6-6331703-T-C
• rs1318606
• ENST00000845977.1:n.808A>G

Variant summary

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

The ENST00000845977.1(ENSG00000309919):​n.808A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,156 control chromosomes in the GnomAD database, including 11,656 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 0.38 (11656 hom., cov: 33)
• Consequence: ENSG00000309919 ENST00000845977.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 17 publications found

Genes affected

ENSG00000309919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000845977.1. 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
	ENSG00000309919	ENST00000845977.1		n.808A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58239 AN: 152038 Hom.: 11659 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.383 AC: 58254 AN: 152156 Hom.: 11656 Cov.: 33 AF XY: 0.382 AC XY: 28437 AN XY: 74354

African (AFR) AF: 0.278 AC: 11545 AN: 41512

American (AMR) AF: 0.397 AC: 6065 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3288 AN: 5180

South Asian (SAS) AF: 0.403 AC: 1941 AN: 4818

European-Finnish (FIN) AF: 0.371 AC: 3917 AN: 10570

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

European-Non Finnish (NFE) AF: 0.425 AC: 28891 AN: 67998

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.408 Hom.: 41880

Bravo AF: 0.384

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.62
PhyloP100		0.32

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: rs1318606;

hg19: chr6-6331936;