3-6240341-G-A

Variant names:

• chr3-6240341-G-A
• rs10490889
• ENST00000435651.2:n.95+91763G>A

Variant summary

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

The ENST00000435651.2(ENSG00000226022):​n.95+91763G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,012 control chromosomes in the GnomAD database, including 8,989 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 0.34 (8989 hom., cov: 33)
• Consequence: ENSG00000226022 ENST00000435651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226022	ENST00000435651.2	TSL:3	n.95+91763G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50938 AN: 151894 Hom.: 8981 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.335 AC: 50986 AN: 152012 Hom.: 8989 Cov.: 33 AF XY: 0.337 AC XY: 25010 AN XY: 74298

African (AFR) AF: 0.251 AC: 10392 AN: 41462

American (AMR) AF: 0.337 AC: 5142 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2392 AN: 5164

South Asian (SAS) AF: 0.368 AC: 1769 AN: 4810

European-Finnish (FIN) AF: 0.398 AC: 4195 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24935 AN: 67970

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.347 Hom.: 1603

Bravo AF: 0.325

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.64
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10490889; hg19: chr3-6282028;