rs1263100

chr2-190759747-A-G

Variant summary

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

The ENST00000676095.2(ENSG00000228509):n.195-20416T>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 0.39 in 151,808 control chromosomes in the GnomAD database, including 12,147 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 0.39 (12147 hom., cov: 30)
• Consequence: ENST00000676095.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907946	XR_007087780.1	n.410+345T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000676095.2	n.195-20416T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59216 AN: 151690 Hom.: 12144 Cov.: 30

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.390 AC: 59234 AN: 151808 Hom.: 12147 Cov.: 30 AF XY: 0.381 AC XY: 28257 AN XY: 74210

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.396

Alfa AF: 0.416 Hom.: 2188

Bravo AF: 0.387

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.75
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1263100; hg19: chr2-191624473;