rs4124862

Variant names:

• chr10-59616970-T-C
• rs4124862
• ENST00000644636.1:n.101-5152T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-59616970-T-C
• chr10-59616970-T-G

Variant summary

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

The ENST00000644636.1(ENSG00000235140):​n.101-5152T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,798 control chromosomes in the GnomAD database, including 14,675 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 0.43 (14675 hom., cov: 30)
• Consequence: ENSG00000235140 ENST00000644636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 2 publications found

Genes affected

ENSG00000235140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235140	ENST00000644636.1		n.101-5152T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64924 AN: 151680 Hom.: 14665 Cov.: 30

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.428 AC: 64982 AN: 151798 Hom.: 14675 Cov.: 30 AF XY: 0.421 AC XY: 31256 AN XY: 74198

African (AFR) AF: 0.584 AC: 24149 AN: 41342

American (AMR) AF: 0.334 AC: 5099 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3464

East Asian (EAS) AF: 0.391 AC: 2012 AN: 5142

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4816

European-Finnish (FIN) AF: 0.351 AC: 3704 AN: 10546

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25953 AN: 67924

Other (OTH) AF: 0.378 AC: 795 AN: 2102

Alfa AF: 0.412 Hom.: 2176

Bravo AF: 0.433

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4124862;

hg19: chr10-61376728;