rs10495499

Positions:

• chr2-4451820-G-C
• chr2-4451820-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000707165.1(ENSG00000291325):​n.506+789G>C 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 0.027 in 152,154 control chromosomes in the GnomAD database, including 86 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 0.027 (86 hom., cov: 32)
• Consequence: ENST00000707165.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.027 (4108/152154) while in subpopulation NFE AF= 0.0439 (2984/67984). AF 95% confidence interval is 0.0426. There are 86 homozygotes in gnomad4. There are 1920 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 86 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707165.1	n.506+789G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4107 AN: 152036 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00691

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0270 AC: 4108 AN: 152154 Hom.: 86 Cov.: 32 AF XY: 0.0258 AC XY: 1920 AN XY: 74396

Gnomad4 AFR AF: 0.00689

Gnomad4 AMR AF: 0.0183

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0427 Hom.: 20

Bravo AF: 0.0237

Asia WGS AF: 0.0100 AC: 36 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495499; hg19: chr2-4499410;