chr3-3421269-A-G

Variant names:

• chr3-3421269-A-G
• rs10510262
• ENST00000420000.6:n.201-38619T>C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-38619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,248 control chromosomes in the GnomAD database, including 507 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 0.060 (507 hom., cov: 33)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 1 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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
ENSG00000223727	ENST00000420000.6	n.201-38619T>C		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.175+19639T>C		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.60-38619T>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9148 AN: 152130 Hom.: 507 Cov.: 33

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0316

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0600 AC: 9142 AN: 152248 Hom.: 507 Cov.: 33 AF XY: 0.0616 AC XY: 4585 AN XY: 74438

African (AFR) AF: 0.0541 AC: 2246 AN: 41528

American (AMR) AF: 0.0473 AC: 723 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0397 AC: 138 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1691 AN: 5172

South Asian (SAS) AF: 0.122 AC: 590 AN: 4828

European-Finnish (FIN) AF: 0.0316 AC: 336 AN: 10626

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3248 AN: 68016

Other (OTH) AF: 0.0487 AC: 103 AN: 2116

Alfa AF: 0.0499 Hom.: 455

Bravo AF: 0.0594

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10510262; hg19: chr3-3462953;