rs11265385

Variant names:

• chr1-160400029-T-G
• rs11265385
• XR_007066686.1:n.481+6143A>C

Variant summary

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

The XR_007066686.1(LOC105371466):​n.481+6143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,028 control chromosomes in the GnomAD database, including 7,879 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 0.31 (7879 hom., cov: 32)
• Consequence: LOC105371466 XR_007066686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 2 publications found

Genes affected

LOC105371466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371466	XR_007066686.1	n.481+6143A>C		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47545 AN: 151910 Hom.: 7881 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47562 AN: 152028 Hom.: 7879 Cov.: 32 AF XY: 0.312 AC XY: 23197 AN XY: 74326

African (AFR) AF: 0.226 AC: 9375 AN: 41466

American (AMR) AF: 0.363 AC: 5545 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 980 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5158

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10584

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23973 AN: 67934

Other (OTH) AF: 0.324 AC: 683 AN: 2108

Alfa AF: 0.325 Hom.: 3134

Bravo AF: 0.316

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.2
DANN	Benign	0.80
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs11265385; hg19: chr1-160369819;