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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370273	XR_942108.4	n.277-331G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;