rs10495505

chr2-4553972-C-T

Variant summary

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

The ENST00000707165.1(ENSG00000291325):n.621+43813C>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 0.276 in 150,650 control chromosomes in the GnomAD database, including 5,772 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 0.28 (5772 hom., cov: 28)
• Consequence: ENST00000707165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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
	ENST00000707165.1	n.621+43813C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41491 AN: 150536 Hom.: 5773 Cov.: 28

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.276 AC: 41517 AN: 150650 Hom.: 5772 Cov.: 28 AF XY: 0.277 AC XY: 20364 AN XY: 73492

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.267

Alfa AF: 0.268 Hom.: 2871

Bravo AF: 0.266

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.44
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495505; hg19: chr2-4601562;