rs12516844

Positions:

• chr5-68742250-T-G

Variant summary

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

The ENST00000688207.1(ENSG00000250237):​n.65+17338A>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 0.103 in 152,040 control chromosomes in the GnomAD database, including 937 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 0.10 (937 hom., cov: 32)
• Consequence: ENST00000688207.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379013	XR_007058804.1	n.440+86458A>C		intron_variant, non_coding_transcript_variant
LOC105379013	XR_007058805.1	n.110+17338A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688207.1	n.65+17338A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15624 AN: 151920 Hom.: 937 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.103 AC: 15640 AN: 152040 Hom.: 937 Cov.: 32 AF XY: 0.104 AC XY: 7704 AN XY: 74326

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0926

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.120

Alfa AF: 0.108 Hom.: 1333

Bravo AF: 0.108

Asia WGS AF: 0.159 AC: 552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12516844; hg19: chr5-68038077;