rs10995356

chr10-62896153-G-Achr10-62896153-G-T

Variant summary

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

The ENST00000493899.2(ENSG00000289487):n.417-1616C>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 0.372 in 151,998 control chromosomes in the GnomAD database, including 12,430 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 0.37 (12430 hom., cov: 32)
• Consequence: ENST00000493899.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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 (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984012	XR_001747465.2	n.424-1616C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000493899.2	n.417-1616C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000690352.1	n.424-601C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56540 AN: 151880 Hom.: 12422 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.372 AC: 56558 AN: 151998 Hom.: 12430 Cov.: 32 AF XY: 0.373 AC XY: 27734 AN XY: 74282

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.416

Alfa AF: 0.460 Hom.: 32454

Bravo AF: 0.368

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995356; hg19: chr10-64655913;