chr10-62730735-C-T

Variant names:

• chr10-62730735-C-T
• rs442309
• ENST00000649548.2:n.160-44656G>A

Variant summary

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

The ENST00000649548.2(ENSG00000238280):​n.160-44656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,754 control chromosomes in the GnomAD database, including 19,971 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 0.51 (19971 hom., cov: 30)
• Consequence: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 17 publications found

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 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
ENSG00000238280	ENST00000649548.2	n.160-44656G>A		intron_variant	Intron 1 of 3
ENSG00000238280	ENST00000821260.1	n.165-1664G>A		intron_variant	Intron 1 of 1
ENSG00000238280	ENST00000821261.1	n.426-1664G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77167 AN: 151642 Hom.: 19950 Cov.: 30

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.509 AC: 77241 AN: 151754 Hom.: 19971 Cov.: 30 AF XY: 0.509 AC XY: 37750 AN XY: 74134

African (AFR) AF: 0.494 AC: 20425 AN: 41342

American (AMR) AF: 0.503 AC: 7669 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1436 AN: 5162

South Asian (SAS) AF: 0.607 AC: 2925 AN: 4818

European-Finnish (FIN) AF: 0.508 AC: 5333 AN: 10502

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36425 AN: 67914

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.524 Hom.: 28577

Bravo AF: 0.502

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs442309; hg19: chr10-64490495;