6-29757162-G-T

Variant names:

• chr6-29757162-G-T
• rs1737078
• ENST00000648999.1:n.355+4235G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648999.1(ENSG00000285761):​n.355+4235G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,952 control chromosomes in the GnomAD database, including 15,406 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 0.45 (15406 hom., cov: 32)
• Consequence: ENSG00000285761 ENST00000648999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

Genes affected

ENSG00000285761 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 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
ENSG00000285761	ENST00000648999.1	n.355+4235G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67992 AN: 151834 Hom.: 15381 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.448 AC: 68061 AN: 151952 Hom.: 15406 Cov.: 32 AF XY: 0.444 AC XY: 32956 AN XY: 74286

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.487

Alfa AF: 0.467 Hom.: 17078

Bravo AF: 0.462

Asia WGS AF: 0.473 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1737078; hg19: chr6-29724939;