rs714389

Variant names:

• chr6-82871628-A-G
• rs714389
• ENST00000759599.1:n.61+4367T>C

Variant summary

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

The ENST00000759599.1(ENSG00000298976):​n.61+4367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,260 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 0.19 (3260 hom., cov: 31)
• Consequence: ENSG00000298976 ENST00000759599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 1 publications found

Genes affected

ENSG00000298976 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298976	ENST00000759599.1	n.61+4367T>C		intron_variant	Intron 1 of 3
ENSG00000298976	ENST00000759602.1	n.286-4358T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28107 AN: 151854 Hom.: 3240 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.185 AC: 28167 AN: 151972 Hom.: 3260 Cov.: 31 AF XY: 0.187 AC XY: 13861 AN XY: 74280

African (AFR) AF: 0.250 AC: 10368 AN: 41458

American (AMR) AF: 0.369 AC: 5614 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.129 AC: 666 AN: 5150

South Asian (SAS) AF: 0.115 AC: 553 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8715 AN: 67962

Other (OTH) AF: 0.193 AC: 406 AN: 2108

Alfa AF: 0.144 Hom.: 393

Bravo AF: 0.213

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		-0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs714389; hg19: chr6-83581347;