8-118904878-A-G

Variant names:

• chr8-118904878-A-G
• rs4407910
• ENST00000625758.3:n.1442-107A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000625758.3(SAMD12-AS1):​n.1442-107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,118 control chromosomes in the GnomAD database, including 10,938 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 (10938 hom., cov: 33)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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.1442-107A>G		intron_variant	Intron 7 of 7	5
SAMD12-AS1	ENST00000658340.1	n.1022-107A>G		intron_variant	Intron 7 of 7
SAMD12-AS1	ENST00000664584.2	n.1095-107A>G		intron_variant	Intron 6 of 6
SAMD12-AS1	ENST00000818910.1	n.239-107A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51890 AN: 152000 Hom.: 10930 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.341 AC: 51905 AN: 152118 Hom.: 10938 Cov.: 33 AF XY: 0.341 AC XY: 25322 AN XY: 74366

African (AFR) AF: 0.0919 AC: 3816 AN: 41536

American (AMR) AF: 0.409 AC: 6244 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1150 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1329 AN: 5170

South Asian (SAS) AF: 0.323 AC: 1556 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5102 AN: 10554

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31321 AN: 67972

Other (OTH) AF: 0.354 AC: 749 AN: 2116

Alfa AF: 0.415 Hom.: 7516

Bravo AF: 0.330

Asia WGS AF: 0.242 AC: 841 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	4.5
DANN	Benign	0.26
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4407910; hg19: chr8-119917117;