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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378102	XR_943213.4	n.559-14725G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288696	ENST00000850151.1	n.106-14725G>A		intron_variant	Intron 1 of 4
ENSG00000288696	ENST00000850152.1	n.166-14725G>A		intron_variant	Intron 1 of 3
ENSG00000288696	ENST00000850153.1	n.550-14725G>A		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs4709819; hg19: chr6-164463355; COSMIC: COSV60300292;