rs10038971

Positions:

• chr5-155096973-T-A
• chr5-155096973-T-C
• chr5-155096973-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000660390.1(ENSG00000287963):​n.281+9263T>A 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 0.364 in 152,088 control chromosomes in the GnomAD database, including 12,104 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 0.36 (12104 hom., cov: 32)
• Consequence: ENST00000660390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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
	ENST00000660390.1	n.281+9263T>A		intron_variant, non_coding_transcript_variant
	ENST00000668848.1	n.179+9263T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55218 AN: 151970 Hom.: 12070 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.364 AC: 55300 AN: 152088 Hom.: 12104 Cov.: 32 AF XY: 0.367 AC XY: 27273 AN XY: 74362

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.349

Alfa AF: 0.316 Hom.: 1123

Bravo AF: 0.369

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10038971; hg19: chr5-154476533;