rs4902141

Positions:

• chr14-62501677-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_943932.3(LOC105370529):​n.126-2364T>C 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 0.0239 in 152,346 control chromosomes in the GnomAD database, including 81 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 0.024 (81 hom., cov: 33)
• Consequence: LOC105370529 XR_943932.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733

Genes affected

LOC105370529 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0239 (3635/152346) while in subpopulation SAS AF= 0.0412 (199/4828). AF 95% confidence interval is 0.0365. There are 81 homozygotes in gnomad4. There are 1768 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 81 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370529	XR_943932.3	n.126-2364T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3623 AN: 152228 Hom.: 79 Cov.: 33

Gnomad AFR AF: 0.00680

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0181

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0241

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0239 AC: 3635 AN: 152346 Hom.: 81 Cov.: 33 AF XY: 0.0237 AC XY: 1768 AN XY: 74500

Gnomad4 AFR AF: 0.00678

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.0241

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0342 Hom.: 108

Bravo AF: 0.0231

Asia WGS AF: 0.0480 AC: 166 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902141; hg19: chr14-62968395;