chr10-124320411-A-C

Variant names:

• chr10-124320411-A-C
• rs4962728
• ENST00000748496.1:n.106-2910T>G

Variant summary

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

The ENST00000748496.1(ENSG00000297515):​n.106-2910T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,056 control chromosomes in the GnomAD database, including 19,146 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 0.50 (19146 hom., cov: 32)
• Consequence: ENSG00000297515 ENST00000748496.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 6 publications found

Genes affected

ENSG00000297515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000748496.1. 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
	ENSG00000297515	ENST00000748496.1		n.106-2910T>G		intron	N/A
	ENSG00000297515	ENST00000748497.1		n.55-2910T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75656 AN: 151938 Hom.: 19148 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.498 AC: 75683 AN: 152056 Hom.: 19146 Cov.: 32 AF XY: 0.496 AC XY: 36828 AN XY: 74308

African (AFR) AF: 0.400 AC: 16576 AN: 41482

American (AMR) AF: 0.497 AC: 7602 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2705 AN: 5172

South Asian (SAS) AF: 0.534 AC: 2570 AN: 4814

European-Finnish (FIN) AF: 0.497 AC: 5237 AN: 10540

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.544 AC: 36987 AN: 67986

Other (OTH) AF: 0.522 AC: 1099 AN: 2106

Alfa AF: 0.430 Hom.: 2549

Bravo AF: 0.494

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.068
DANN	Benign	0.35
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4962728; hg19: chr10-126008980;