rs10955900

Variant names:

• chr8-118792647-G-A
• rs10955900
• ENST00000625758.3:n.1320+28263G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+28263G>A		intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1	n.496-65410G>A		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.900+28263G>A		intron_variant	Intron 6 of 7
SAMD12-AS1	ENST00000664584.1	n.760+28263G>A		intron_variant	Intron 5 of 6

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;