rs11242704

Variant names:

• chr6-1535763-A-G
• rs11242704
• ENST00000607350.2:n.129-6584T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-1535763-A-G
• chr6-1535763-A-T

Variant summary

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

The ENST00000808963.1(ENSG00000272279):​n.224-6584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,848 control chromosomes in the GnomAD database, including 15,936 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 0.42 (15936 hom., cov: 30)
• Consequence: ENSG00000272279 ENST00000808963.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 12 publications found

Genes affected

ENSG00000272279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808963.1. 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
	ENSG00000272279	ENST00000607350.2	TSL:6	n.129-6584T>C		intron	N/A
	ENSG00000272279	ENST00000808963.1		n.224-6584T>C		intron	N/A
	ENSG00000272279	ENST00000808964.1		n.211-6608T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64301 AN: 151730 Hom.: 15907 Cov.: 30

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.424 AC: 64374 AN: 151848 Hom.: 15936 Cov.: 30 AF XY: 0.421 AC XY: 31248 AN XY: 74208

African (AFR) AF: 0.693 AC: 28662 AN: 41352

American (AMR) AF: 0.308 AC: 4697 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1028 AN: 3464

East Asian (EAS) AF: 0.475 AC: 2454 AN: 5164

South Asian (SAS) AF: 0.372 AC: 1790 AN: 4812

European-Finnish (FIN) AF: 0.314 AC: 3307 AN: 10526

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21144 AN: 67958

Other (OTH) AF: 0.389 AC: 819 AN: 2106

Alfa AF: 0.357 Hom.: 23933

Bravo AF: 0.436

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.40

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: rs11242704;

hg19: chr6-1535998;