rs7992626

chr13-67841275-C-T

Variant summary

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

The XR_942050.2(LOC105370251):n.183+16697G>A 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 0.183 in 152,096 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: LOC105370251 XR_942050.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

LOC105370251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370251	XR_942050.2	n.183+16697G>A		intron_variant, non_coding_transcript_variant
LOC105370251	XR_942049.3	n.183+16697G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27802 AN: 151976 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.183 AC: 27868 AN: 152096 Hom.: 2640 Cov.: 32 AF XY: 0.181 AC XY: 13427 AN XY: 74332

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.216

Alfa AF: 0.188 Hom.: 621

Bravo AF: 0.188

Asia WGS AF: 0.208 AC: 720 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7992626; hg19: chr13-68415407; COSMIC: COSV68422071;