chr14-77261503-C-T

Position:

• chr14-77261503-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064276.1(LOC124903351):​n.1324+361C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124903351	XR_007064276.1	n.1324+361C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.254

Alfa AF: 0.229 Hom.: 2541

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs368855; hg19: chr14-77727846;