rs2635556

chr14-19944880-T-C

Variant summary

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

The XR_007064055.1(LOC124903278):n.49-1039A>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 0.307 in 148,858 control chromosomes in the GnomAD database, including 4,698 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 0.31 (4698 hom., cov: 38)
• Consequence: LOC124903278 XR_007064055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC124903278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903278	XR_007064055.1	n.49-1039A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.307 AC: 45702 AN: 148734 Hom.: 4698 Cov.: 38

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.307 AC: 45707 AN: 148858 Hom.: 4698 Cov.: 38 AF XY: 0.308 AC XY: 22378 AN XY: 72740

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.340

Alfa AF: 0.345 Hom.: 633

Asia WGS AF: 0.340 AC: 1176 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.0
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2635556; hg19: chr14-20413039;