3-6336008-A-T

Variant names:

• chr3-6336008-A-T
• rs271066
• ENST00000435651.1:n.96-22893A>T

Variant summary

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

The ENST00000435651.1(ENSG00000226022):​n.96-22893A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,038 control chromosomes in the GnomAD database, including 13,691 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 0.39 (13691 hom., cov: 32)
• Consequence: ENSG00000226022 ENST00000435651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

ENSG00000226022 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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
ENSG00000226022	ENST00000435651.1	n.96-22893A>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59610 AN: 151920 Hom.: 13692 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.392 AC: 59617 AN: 152038 Hom.: 13691 Cov.: 32 AF XY: 0.397 AC XY: 29526 AN XY: 74302

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.419

Alfa AF: 0.483 Hom.: 10203

Bravo AF: 0.374

Asia WGS AF: 0.425 AC: 1477 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs271066; hg19: chr3-6377695;