rs1366750

Variant names:

• chr2-154482647-G-A
• rs1366750
• XR_923485.4:n.115+6137C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_923485.4(LOC105373694):​n.115+6137C>T variant causes a intron 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_923485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

Genes affected

LOC105373694 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105373694	XR_923485.4	n.115+6137C>T		intron_variant	Intron 1 of 2
LOC105373694	XR_923486.4	n.115+6137C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0942 AC: 3909 AN: 41502

American (AMR) AF: 0.222 AC: 3396 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2094 AN: 5136

South Asian (SAS) AF: 0.166 AC: 799 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1495 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10395 AN: 67988

Other (OTH) AF: 0.162 AC: 342 AN: 2114

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1366750; hg19: chr2-155339159;