rs4709819

Variant names:

• chr6-164042323-G-A
• rs4709819
• ENST00000850151.1:n.106-14725G>A

Variant summary

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

The ENST00000850151.1(ENSG00000288696):​n.106-14725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,020 control chromosomes in the GnomAD database, including 13,172 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 (13172 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 14 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850151.1. 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
	ENSG00000288696	ENST00000850151.1		n.106-14725G>A		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.166-14725G>A		intron	N/A
	ENSG00000288696	ENST00000850153.1		n.550-14725G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63122 AN: 151902 Hom.: 13151 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.416 AC: 63180 AN: 152020 Hom.: 13172 Cov.: 32 AF XY: 0.421 AC XY: 31262 AN XY: 74320

African (AFR) AF: 0.380 AC: 15763 AN: 41450

American (AMR) AF: 0.457 AC: 6975 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2249 AN: 5166

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4812

European-Finnish (FIN) AF: 0.488 AC: 5155 AN: 10566

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.415 AC: 28193 AN: 67964

Other (OTH) AF: 0.406 AC: 858 AN: 2114

Alfa AF: 0.416 Hom.: 57493

Bravo AF: 0.414

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		-2.5

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: rs4709819;

hg19: chr6-164463355;

COSMIC: COSV60300292;