rs1553460

Variant names:

• chr4-18194238-T-A
• rs1553460
• XR_001741599.2:n.1697T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-18194238-T-A
• chr4-18194238-T-C
• chr4-18194238-T-G

Variant summary

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

The XR_001741599.2(LOC107986262):​n.1697T>A 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 0.757 in 152,086 control chromosomes in the GnomAD database, including 43,694 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 0.76 (43694 hom., cov: 32)
• Consequence: LOC107986262 XR_001741599.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 7 publications found

Genes affected

LOC107986262 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986262	XR_001741599.2	n.1697T>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107986262	XR_001741600.2	n.1666T>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107986262	XR_001741598.1	n.1473+3927T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303707	ENST00000796675.1	n.486+3927T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114959 AN: 151968 Hom.: 43641 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.757 AC: 115075 AN: 152086 Hom.: 43694 Cov.: 32 AF XY: 0.758 AC XY: 56368 AN XY: 74328

African (AFR) AF: 0.805 AC: 33381 AN: 41478

American (AMR) AF: 0.820 AC: 12534 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2611 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4432 AN: 5156

South Asian (SAS) AF: 0.825 AC: 3988 AN: 4832

European-Finnish (FIN) AF: 0.690 AC: 7293 AN: 10568

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48382 AN: 67976

Other (OTH) AF: 0.760 AC: 1605 AN: 2112

Alfa AF: 0.731 Hom.: 5089

Bravo AF: 0.769

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs1553460; hg19: chr4-18195861;