rs4124862

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000644636.1(ENSG00000235140):​n.101-5152T>C variant causes a intron, non coding transcript 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: ENST00000644636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644636.1	n.101-5152T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.378

Alfa AF: 0.407 Hom.: 2046

Bravo AF: 0.433

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4124862; hg19: chr10-61376728;