rs10955900

chr8-118792647-G-A

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):n.1320+28263G>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 0.336 in 151,882 control chromosomes in the GnomAD database, including 10,349 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 0.34 (10349 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+28263G>A		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000629661.1	n.496-65410G>A		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000658340.1	n.900+28263G>A		intron_variant, non_coding_transcript_variant
SAMD12-AS1	ENST00000664584.1	n.760+28263G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51023 AN: 151764 Hom.: 10345 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.336 AC: 51036 AN: 151882 Hom.: 10349 Cov.: 32 AF XY: 0.333 AC XY: 24716 AN XY: 74212

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.359

Alfa AF: 0.400 Hom.: 1674

Bravo AF: 0.325

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	7.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10955900; hg19: chr8-119804886;