rs1186868

Positions:

• chr2-61764103-G-A
• chr2-61764103-G-T

Variant summary

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

The ENST00000689428.1(ENSG00000289410):​n.99C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,236 control chromosomes in the GnomAD database, including 429 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 0.069 (429 hom., cov: 32)
• Consequence: ENST00000689428.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985767	XR_001739092.2	n.161C>T		non_coding_transcript_exon_variant	1/2
LOC107985767	XR_007086333.1	n.161C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689428.1	n.99C>T		non_coding_transcript_exon_variant	1/2
	ENST00000687336.1	n.203C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10458 AN: 152118 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0687 AC: 10461 AN: 152236 Hom.: 429 Cov.: 32 AF XY: 0.0662 AC XY: 4931 AN XY: 74432

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0548 Hom.: 108

Bravo AF: 0.0711

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1186868; hg19: chr2-61991238;