6-81477120-C-T

Variant names:

• chr6-81477120-C-T
• rs1321761
• ENST00000759357.1:n.200-31060G>A

Variant summary

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

The ENST00000759357.1(ENSG00000298959):​n.200-31060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 150,774 control chromosomes in the GnomAD database, including 19,920 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 0.50 (19920 hom., cov: 30)
• Consequence: ENSG00000298959 ENST00000759357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 1 publications found

Genes affected

ENSG00000298959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759357.1. 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
	ENSG00000298959	ENST00000759357.1		n.200-31060G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76119 AN: 150656 Hom.: 19924 Cov.: 30

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.505 AC: 76125 AN: 150774 Hom.: 19920 Cov.: 30 AF XY: 0.504 AC XY: 37048 AN XY: 73562

African (AFR) AF: 0.363 AC: 14959 AN: 41246

American (AMR) AF: 0.532 AC: 8014 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1835 AN: 3442

East Asian (EAS) AF: 0.448 AC: 2280 AN: 5090

South Asian (SAS) AF: 0.504 AC: 2424 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5328 AN: 10420

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39545 AN: 67402

Other (OTH) AF: 0.496 AC: 1037 AN: 2092

Alfa AF: 0.550 Hom.: 12194

Bravo AF: 0.503

Asia WGS AF: 0.452 AC: 1574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		0.56

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: rs1321761;

hg19: chr6-82186837;