XR_007064152.1:n.221+11278G>T

Variant names:

• chr14-49140552-C-A
• rs8008169
• XR_007064152.1:n.221+11278G>T

Variant summary

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

The XR_007064152.1(LOC105378178):​n.221+11278G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,728 control chromosomes in the GnomAD database, including 11,038 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 0.37 (11038 hom., cov: 32)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 1 publications found

Genes affected

LOC105378178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.221+11278G>T		intron_variant	Intron 3 of 9
LOC105378178	XR_007064153.1	n.221+11278G>T		intron_variant	Intron 3 of 4
LOC105378178	XR_943837.3	n.221+11278G>T		intron_variant	Intron 3 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55614 AN: 151612 Hom.: 11029 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.367 AC: 55645 AN: 151728 Hom.: 11038 Cov.: 32 AF XY: 0.367 AC XY: 27220 AN XY: 74168

African (AFR) AF: 0.276 AC: 11421 AN: 41430

American (AMR) AF: 0.530 AC: 8057 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3460

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4821 AN: 10516

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27513 AN: 67806

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.368 Hom.: 1635

Bravo AF: 0.372

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs8008169; hg19: chr14-49607270;