rs1476896

Positions:

• chr2-190759793-A-G

Variant summary

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

The ENST00000676095.2(ENSG00000228509):​n.195-20462T>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 0.26 in 152,004 control chromosomes in the GnomAD database, including 5,509 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 0.26 (5509 hom., cov: 32)
• Consequence: ENST00000676095.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124907946	XR_007087780.1	n.410+299T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000676095.2	n.195-20462T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39562 AN: 151886 Hom.: 5504 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.260 AC: 39585 AN: 152004 Hom.: 5509 Cov.: 32 AF XY: 0.264 AC XY: 19575 AN XY: 74276

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.253

Alfa AF: 0.278 Hom.: 5537

Bravo AF: 0.242

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.35
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476896; hg19: chr2-191624519;