chr8-118821226-T-G

Variant names:

• chr8-118821226-T-G
• rs1389545
• ENST00000625758.3:n.1320+56842T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000625758.3(SAMD12-AS1):​n.1320+56842T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 142,800 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 (0 hom., cov: 30)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

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

ENSG00000306504 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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+56842T>G		intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1	n.496-36831T>G		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.900+56842T>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.0000140 AC: 2 AN: 142692 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000492

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000140 AC: 2 AN: 142800 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 69342

African (AFR) AF: 0.0000491 AC: 2 AN: 40760

American (AMR) AF: 0.00 AC: 0 AN: 13972

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3008

East Asian (EAS) AF: 0.00 AC: 0 AN: 4414

South Asian (SAS) AF: 0.00 AC: 0 AN: 4070

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9374

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 248

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64126

Other (OTH) AF: 0.00 AC: 0 AN: 1940

Alfa AF: 0.00 Hom.: 771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1389545; hg19: chr8-119833465;