XR_007064276.1:n.1324+361C>T

Variant names:

• chr14-77261503-C-T
• rs368855
• XR_007064276.1:n.1324+361C>T

Variant summary

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

The XR_007064276.1(LOC124903351):​n.1324+361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,128 control chromosomes in the GnomAD database, including 4,786 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 0.24 (4786 hom., cov: 33)
• Consequence: LOC124903351 XR_007064276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 5 publications found

Genes affected

LOC124903351 (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 = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903351	XR_007064276.1	n.1324+361C>T		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35867 AN: 152010 Hom.: 4777 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.236 AC: 35902 AN: 152128 Hom.: 4786 Cov.: 33 AF XY: 0.241 AC XY: 17914 AN XY: 74364

African (AFR) AF: 0.197 AC: 8167 AN: 41478

American (AMR) AF: 0.313 AC: 4793 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3050 AN: 5162

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4818

European-Finnish (FIN) AF: 0.188 AC: 1995 AN: 10590

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14529 AN: 67994

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.227 Hom.: 3311

Bravo AF: 0.248

Asia WGS AF: 0.391 AC: 1363 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	0.37
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs368855; hg19: chr14-77727846;