rs11988997

chr8-118753955-C-T

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):n.1205-10314C>T 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 0.0739 in 152,112 control chromosomes in the GnomAD database, including 425 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 0.074 (425 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

SAMD12-AS1 (HGNC:30937): (SAMD12 antisense RNA 1)

LOC124902007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.085 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902007	XR_007061074.1	n.86-27G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1205-10314C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11240 AN: 151994 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.0926

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0739 AC: 11245 AN: 152112 Hom.: 425 Cov.: 32 AF XY: 0.0732 AC XY: 5443 AN XY: 74362

Gnomad4 AFR AF: 0.0766

Gnomad4 AMR AF: 0.0638

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.0703

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0751 Hom.: 636

Bravo AF: 0.0738

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11988997; hg19: chr8-119766194;