6-68158440-G-T

Variant names:

• chr6-68158440-G-T
• rs777649
• ENST00000718116.1:n.418-64229G>T

Variant summary

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

The ENST00000718116.1(ENSG00000285838):​n.418-64229G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,928 control chromosomes in the GnomAD database, including 12,350 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 0.40 (12350 hom., cov: 32)
• Consequence: ENSG00000285838 ENST00000718116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 4 publications found

Genes affected

ENSG00000285838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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
ENSG00000285838	ENST00000718116.1	n.418-64229G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60562 AN: 151810 Hom.: 12337 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.399 AC: 60606 AN: 151928 Hom.: 12350 Cov.: 32 AF XY: 0.398 AC XY: 29575 AN XY: 74236

African (AFR) AF: 0.353 AC: 14632 AN: 41448

American (AMR) AF: 0.304 AC: 4644 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1685 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2162 AN: 5150

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4814

European-Finnish (FIN) AF: 0.450 AC: 4736 AN: 10536

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29387 AN: 67926

Other (OTH) AF: 0.388 AC: 818 AN: 2108

Alfa AF: 0.415 Hom.: 39000

Bravo AF: 0.383

Asia WGS AF: 0.384 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs777649; hg19: chr6-68868332;