rs10503657

chr8-19184809-G-A

Variant summary

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

The NR_038919.1(LOC100128993):n.569-147C>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 0.188 in 152,184 control chromosomes in the GnomAD database, including 3,090 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 0.19 (3090 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LOC100128993 NR_038919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100128993	NR_038919.1	n.569-147C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520920.5	n.474+42359C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000517949.5	n.535+42359C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000518417.1	n.279-147C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28548 AN: 152062 Hom.: 3079 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.0785

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.188 AC: 28594 AN: 152180 Hom.: 3090 Cov.: 32 AF XY: 0.187 AC XY: 13886 AN XY: 74410

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.0785

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.183

Alfa AF: 0.160 Hom.: 990

Bravo AF: 0.206

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.67
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503657; hg19: chr8-19042319;