6-14636732-T-C

Variant names:

• chr6-14636732-T-C
• rs707824
• ENST00000702111.1:n.156+7219A>G

Variant summary

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

The ENST00000702111.1(ENSG00000234261):​n.156+7219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,180 control chromosomes in the GnomAD database, including 47,369 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 0.75 (47369 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000702111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 18 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702111.1. 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
	ENSG00000234261	ENST00000702111.1		n.156+7219A>G		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.229+7219A>G		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.165+7219A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113617 AN: 152062 Hom.: 47372 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.747 AC: 113639 AN: 152180 Hom.: 47369 Cov.: 32 AF XY: 0.751 AC XY: 55910 AN XY: 74414

African (AFR) AF: 0.344 AC: 14245 AN: 41450

American (AMR) AF: 0.829 AC: 12687 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2925 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5160 AN: 5178

South Asian (SAS) AF: 0.834 AC: 4027 AN: 4826

European-Finnish (FIN) AF: 0.935 AC: 9923 AN: 10618

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61950 AN: 68016

Other (OTH) AF: 0.778 AC: 1645 AN: 2114

Alfa AF: 0.833 Hom.: 132792

Bravo AF: 0.723

Asia WGS AF: 0.880 AC: 3060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.85
PhyloP100		-0.90

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: rs707824;

hg19: chr6-14636963;