8-118821226-T-C

Position:

• chr8-118821226-T-C

Variant summary

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

The variant allele was found at a frequency of 0.811 in 142,742 control chromosomes in the GnomAD database, including 44,611 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 0.81 (44611 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118821226T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+56842T>C		intron_variant		5
SAMD12-AS1	ENST00000629661.1	n.496-36831T>C		intron_variant		5
SAMD12-AS1	ENST00000658340.1	n.900+56842T>C		intron_variant
SAMD12-AS1	ENST00000664584.1	n.760+56842T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.810 AC: 115602 AN: 142634 Hom.: 44554 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.811 AC: 115713 AN: 142742 Hom.: 44611 Cov.: 30 AF XY: 0.804 AC XY: 55750 AN XY: 69302

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.796

Alfa AF: 0.604 Hom.: 771

Bravo AF: 0.768

Asia WGS AF: 0.620 AC: 1978 AN: 3184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1389545; hg19: chr8-119833465;