rs9377063

Variant names:

• chr6-147613811-G-A
• rs9377063
• ENST00000566741.1:c.162+104424G>A

Variant summary

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

The ENST00000566741.1(SAMD5):​c.162+104424G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,516 control chromosomes in the GnomAD database, including 11,201 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 0.37 (11201 hom., cov: 31)
• Consequence: SAMD5 ENST00000566741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 6 publications found

Genes affected

SAMD5 (HGNC:21180): (sterile alpha motif domain containing 5) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD5	XM_017010850.2	c.459+104424G>A		intron_variant	Intron 1 of 1		XP_016866339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD5	ENST00000566741.1	c.162+104424G>A		intron_variant	Intron 1 of 1	3		ENSP00000456528.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56419 AN: 151398 Hom.: 11186 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.373 AC: 56468 AN: 151516 Hom.: 11201 Cov.: 31 AF XY: 0.372 AC XY: 27561 AN XY: 74062

African (AFR) AF: 0.460 AC: 18886 AN: 41040

American (AMR) AF: 0.303 AC: 4620 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.101 AC: 518 AN: 5154

South Asian (SAS) AF: 0.201 AC: 970 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4592 AN: 10534

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24649 AN: 67930

Other (OTH) AF: 0.356 AC: 751 AN: 2108

Alfa AF: 0.359 Hom.: 19974

Bravo AF: 0.365

Asia WGS AF: 0.177 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.53
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs9377063; hg19: chr6-147934947;