6-51310444-C-T

Variant names:

• chr6-51310444-C-T
• rs1327261
• ENST00000726598.1:n.243-8097G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000726598.1(ENSG00000294896):​n.243-8097G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,564 control chromosomes in the GnomAD database, including 3,365 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 0.15 (3365 hom., cov: 32)
• Consequence: ENSG00000294896 ENST00000726598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687
• Publications: 2 publications found

Genes affected

ENSG00000294896 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726598.1. 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
	ENSG00000294896	ENST00000726598.1		n.243-8097G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23214 AN: 151446 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.0817

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.153 AC: 23251 AN: 151564 Hom.: 3365 Cov.: 32 AF XY: 0.150 AC XY: 11093 AN XY: 74050

African (AFR) AF: 0.384 AC: 15847 AN: 41302

American (AMR) AF: 0.0936 AC: 1423 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0817 AC: 283 AN: 3462

East Asian (EAS) AF: 0.0597 AC: 306 AN: 5124

South Asian (SAS) AF: 0.0828 AC: 398 AN: 4806

European-Finnish (FIN) AF: 0.0507 AC: 537 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0611 AC: 4140 AN: 67764

Other (OTH) AF: 0.131 AC: 276 AN: 2104

Alfa AF: 0.0761 Hom.: 596

Bravo AF: 0.166

Asia WGS AF: 0.0890 AC: 311 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	24
DANN	Benign	0.58
PhyloP100		0.69

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: rs1327261;

hg19: chr6-51175242;