rs12103757

Positions:

• chr17-70478692-A-G

Variant summary

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

The XR_007065977.1(LOC124904100):​n.79-23351A>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 0.511 in 152,018 control chromosomes in the GnomAD database, including 20,143 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 0.51 (20143 hom., cov: 32)
• Consequence: LOC124904100 XR_007065977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

LOC124904100 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904100	XR_007065977.1	n.79-23351A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77618 AN: 151900 Hom.: 20111 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.511 AC: 77708 AN: 152018 Hom.: 20143 Cov.: 32 AF XY: 0.509 AC XY: 37835 AN XY: 74300

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.536

Alfa AF: 0.510 Hom.: 2465

Bravo AF: 0.527

Asia WGS AF: 0.679 AC: 2349 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12103757; hg19: chr17-68474833;