rs16891338

Positions:

• chr8-118658958-A-G

Variant summary

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

The NR_038210.1(SAMD12-AS1):​n.308-9492A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,002 control chromosomes in the GnomAD database, including 2,416 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 0.11 (2416 hom., cov: 32)
• Consequence: SAMD12-AS1 NR_038210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

SAMD12-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD12-AS1	NR_038210.1	n.308-9492A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.811-9492A>G		intron_variant		5
SAMD12-AS1	ENST00000629661.1	n.102-9492A>G		intron_variant		5
SAMD12-AS1	ENST00000658340.1	n.263-9492A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17018 AN: 151884 Hom.: 2414 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0277

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0873

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

GnomAD4 genome AF: 0.112 AC: 17046 AN: 152002 Hom.: 2416 Cov.: 32 AF XY: 0.108 AC XY: 8050 AN XY: 74284

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0273

Gnomad4 FIN AF: 0.0108

Gnomad4 NFE AF: 0.0252

Gnomad4 OTH AF: 0.0864

Alfa AF: 0.0775 Hom.: 210

Bravo AF: 0.126

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
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: rs16891338; hg19: chr8-119671197;