6-127114919-C-T

Variant names:

• chr6-127114919-C-T
• rs1936800
• ENST00000650648.1:n.402-43833G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000650648.1(ENSG00000293110):​n.402-43833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,074 control chromosomes in the GnomAD database, including 19,937 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 0.51 (19937 hom., cov: 33)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 64 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650648.1. 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
	ENSG00000293110	ENST00000650648.1		n.402-43833G>A		intron	N/A
	ENSG00000293110	ENST00000650684.1		n.474-43833G>A		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.441-43833G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77826 AN: 151954 Hom.: 19920 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.512 AC: 77892 AN: 152074 Hom.: 19937 Cov.: 33 AF XY: 0.508 AC XY: 37756 AN XY: 74328

African (AFR) AF: 0.540 AC: 22404 AN: 41478

American (AMR) AF: 0.476 AC: 7279 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1558 AN: 3466

East Asian (EAS) AF: 0.522 AC: 2700 AN: 5170

South Asian (SAS) AF: 0.497 AC: 2394 AN: 4814

European-Finnish (FIN) AF: 0.461 AC: 4874 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35156 AN: 67976

Other (OTH) AF: 0.485 AC: 1024 AN: 2112

Alfa AF: 0.517 Hom.: 28792

Bravo AF: 0.514

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		0.14

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: rs1936800;

hg19: chr6-127436064;

COSMIC: COSV63150114;