rs723268

chr8-118154455-T-Cchr8-118154455-T-G

Variant summary

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

The NR_146234.2(SAMD12):n.611-9072A>G 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 0.73 in 152,128 control chromosomes in the GnomAD database, including 42,135 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 0.73 (42135 hom., cov: 32)
• Consequence: SAMD12 NR_146234.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

SAMD12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD12	NR_146234.2	n.611-9072A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.730 AC: 111037 AN: 152010 Hom.: 42129 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.730 AC: 111084 AN: 152128 Hom.: 42135 Cov.: 32 AF XY: 0.729 AC XY: 54245 AN XY: 74366

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.735

Alfa AF: 0.789 Hom.: 5700

Bravo AF: 0.712

Asia WGS AF: 0.651 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.2
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723268; hg19: chr8-119166694;