chr10-62707042-A-G

Variant names:

• chr10-62707042-A-G
• rs224135
• ENST00000649548.2:n.160-20963T>C

Variant summary

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

The ENST00000649548.2(ENSG00000238280):​n.160-20963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,062 control chromosomes in the GnomAD database, including 37,018 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 0.68 (37018 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000649548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 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.160-20963T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103128 AN: 151944 Hom.: 36949 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.679 AC: 103258 AN: 152062 Hom.: 37018 Cov.: 32 AF XY: 0.675 AC XY: 50178 AN XY: 74308

African (AFR) AF: 0.925 AC: 38429 AN: 41528

American (AMR) AF: 0.589 AC: 8987 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1831 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2273 AN: 5164

South Asian (SAS) AF: 0.683 AC: 3299 AN: 4830

European-Finnish (FIN) AF: 0.576 AC: 6070 AN: 10532

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40303 AN: 67960

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.619 Hom.: 23664

Bravo AF: 0.685

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs224135; hg19: chr10-64466802;