6-4700910-G-T

Variant names:

• chr6-4700910-G-T
• rs4959312
• ENST00000716074.1:n.601+17617C>A

Variant summary

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

The ENST00000716074.1(ENSG00000284823):​n.601+17617C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 150,662 control chromosomes in the GnomAD database, including 19,391 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 (19391 hom., cov: 27)
• Consequence: ENSG00000284823 ENST00000716074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

Genes affected

ENSG00000284823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716074.1. 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
	ENSG00000284823	ENST00000716074.1		n.601+17617C>A		intron	N/A
	ENSG00000284823	ENST00000827029.1		n.544-7735C>A		intron	N/A
	ENSG00000284823	ENST00000827030.1		n.476-3769C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75329 AN: 150554 Hom.: 19386 Cov.: 27

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.500 AC: 75368 AN: 150662 Hom.: 19391 Cov.: 27 AF XY: 0.504 AC XY: 37086 AN XY: 73542

African (AFR) AF: 0.379 AC: 15595 AN: 41144

American (AMR) AF: 0.575 AC: 8683 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1635 AN: 3462

East Asian (EAS) AF: 0.461 AC: 2359 AN: 5118

South Asian (SAS) AF: 0.585 AC: 2797 AN: 4782

European-Finnish (FIN) AF: 0.580 AC: 5893 AN: 10154

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.543 AC: 36706 AN: 67596

Other (OTH) AF: 0.501 AC: 1049 AN: 2094

Alfa AF: 0.527 Hom.: 82211

Bravo AF: 0.491

Asia WGS AF: 0.557 AC: 1936 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.16
PhyloP100		-2.0

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: rs4959312;

hg19: chr6-4701144;