6-147538512-T-G

Position:

• chr6-147538512-T-G

Variant summary

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

The NM_001030060.3(SAMD5):​c.460-25882T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,070 control chromosomes in the GnomAD database, including 19,361 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 0.50 (19361 hom., cov: 33)
• Consequence: SAMD5 NM_001030060.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD5	NM_001030060.3	c.460-25882T>G		intron_variant		ENST00000367474.2	NP_001025231.1
SAMD5	XM_017010850.2	c.459+29125T>G		intron_variant			XP_016866339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD5	ENST00000367474.2	c.460-25882T>G		intron_variant		2	NM_001030060.3	ENSP00000356444.1
SAMD5	ENST00000566741.1	c.162+29125T>G		intron_variant		3		ENSP00000456528.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75406 AN: 151952 Hom.: 19356 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.496 AC: 75435 AN: 152070 Hom.: 19361 Cov.: 33 AF XY: 0.501 AC XY: 37204 AN XY: 74332

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.506

Alfa AF: 0.505 Hom.: 2406

Bravo AF: 0.486

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2092447; hg19: chr6-147859648;