rs1988623

Variant names:

• chr4-9144727-T-C
• rs1988623
• XR_001741580.3:n.1087A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-9144727-T-C
• chr4-9144727-T-G

Variant summary

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

The XR_001741580.3(LOC105369250):​n.1087A>G 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 0.413 in 151,844 control chromosomes in the GnomAD database, including 15,556 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 0.41 (15556 hom., cov: 33)
• Consequence: LOC105369250 XR_001741580.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

LOC105369250 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369250	XR_001741580.3	n.1087A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105369250	XR_001741581.3	n.1180A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105369250	XR_001741583.3	n.1083A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288075	ENST00000659603.1	n.324+6368A>G		intron_variant	Intron 1 of 2
ENSG00000288075	ENST00000664986.1	n.54+6661A>G		intron_variant	Intron 1 of 1
ENSG00000288075	ENST00000666840.1	n.487-80397A>G		intron_variant	Intron 2 of 3
ENSG00000288075	ENST00000668176.1	n.607+6368A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62622 AN: 151728 Hom.: 15500 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.413 AC: 62746 AN: 151844 Hom.: 15556 Cov.: 33 AF XY: 0.413 AC XY: 30637 AN XY: 74206

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.389

Alfa AF: 0.176 Hom.: 308

Bravo AF: 0.430

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1988623; hg19: chr4-9146453;