rs10518603

Positions:

• chr4-132039903-C-A

Variant summary

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

The ENST00000652009.1(ENSG00000251598):​n.178-11422G>T 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 0.1 in 151,968 control chromosomes in the GnomAD database, including 947 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 0.10 (947 hom., cov: 32)
• Consequence: ENST00000652009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377428	XR_939203.4	n.77-5947G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652009.1	n.178-11422G>T		intron_variant, non_coding_transcript_variant
	ENST00000420721.2	n.182-11422G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15208 AN: 151850 Hom.: 939 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.100 AC: 15248 AN: 151968 Hom.: 947 Cov.: 32 AF XY: 0.100 AC XY: 7442 AN XY: 74262

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0825

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0820 Hom.: 255

Bravo AF: 0.102

Asia WGS AF: 0.0890 AC: 312 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518603; hg19: chr4-132961058;