rs1957636

Positions:

• chr14-54093300-T-C

Variant summary

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

The XR_943883.3(LOC105370507):​n.665-48169A>G 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 0.477 in 151,874 control chromosomes in the GnomAD database, including 19,021 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 0.48 (19021 hom., cov: 31)
• Consequence: LOC105370507 XR_943883.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

LOC105370507 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370507	XR_943883.3	n.665-48169A>G		intron_variant, non_coding_transcript_variant
LOC105370507	XR_943882.3	n.665-1203A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72385 AN: 151756 Hom.: 19022 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.477 AC: 72393 AN: 151874 Hom.: 19021 Cov.: 31 AF XY: 0.475 AC XY: 35264 AN XY: 74226

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.519

Alfa AF: 0.575 Hom.: 36979

Bravo AF: 0.462

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957636; hg19: chr14-54560018;