rs1366750

Positions:

• chr2-154482647-G-A
• chr2-154482647-G-T

Variant summary

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

The XR_923486.4(LOC105373694):​n.115+6137C>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 0.152 in 152,064 control chromosomes in the GnomAD database, including 2,031 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 0.15 (2031 hom., cov: 32)
• Consequence: LOC105373694 XR_923486.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

LOC105373694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373694	XR_923486.4	n.115+6137C>T		intron_variant, non_coding_transcript_variant
LOC105373694	XR_923485.4	n.115+6137C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23064 AN: 151946 Hom.: 2018 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.152 AC: 23090 AN: 152064 Hom.: 2031 Cov.: 32 AF XY: 0.154 AC XY: 11454 AN XY: 74314

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.162

Alfa AF: 0.148 Hom.: 255

Bravo AF: 0.157

Asia WGS AF: 0.225 AC: 778 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1366750; hg19: chr2-155339159;