3-6336008-A-T

Variant names:

• chr3-6336008-A-T
• rs271066
• ENST00000435651.2:n.96-22893A>T

Variant summary

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

The ENST00000435651.2(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 ENST00000435651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 4 publications found

Genes affected

ENSG00000226022 (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 (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435651.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226022	ENST00000435651.2	TSL:3	n.96-22893A>T		intron	N/A

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

African (AFR) AF: 0.137 AC: 5690 AN: 41518

American (AMR) AF: 0.394 AC: 6008 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1990 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2465 AN: 5166

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4828

European-Finnish (FIN) AF: 0.515 AC: 5418 AN: 10528

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34343 AN: 67966

Other (OTH) AF: 0.419 AC: 886 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.64
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs271066;

hg19: chr3-6377695;