rs1341139

Variant names:

• chr13-78967053-C-A
• rs1341139
• XR_942108.4:n.277-331G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-78967053-C-A
• chr13-78967053-C-G
• chr13-78967053-C-T

Variant summary

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

The XR_942108.4(LOC105370273):​n.277-331G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 152,236 control chromosomes in the GnomAD database, including 69,593 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 0.96 (69593 hom., cov: 31)
• Consequence: LOC105370273 XR_942108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 0 publications found

Genes affected

LOC105370273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.956 AC: 145390 AN: 152118 Hom.: 69544 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.956 AC: 145494 AN: 152236 Hom.: 69593 Cov.: 31 AF XY: 0.956 AC XY: 71150 AN XY: 74428

African (AFR) AF: 0.919 AC: 38192 AN: 41554

American (AMR) AF: 0.973 AC: 14878 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3317 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5170

South Asian (SAS) AF: 0.965 AC: 4650 AN: 4820

European-Finnish (FIN) AF: 0.985 AC: 10452 AN: 10616

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65752 AN: 67998

Other (OTH) AF: 0.956 AC: 2017 AN: 2110

Alfa AF: 0.958 Hom.: 17485

Bravo AF: 0.953

Asia WGS AF: 0.978 AC: 3403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1341139; hg19: chr13-79541188;