rs2169826

Positions:

• chr6-130300101-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001258275.3(SAMD3):​c.-188+12877A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 152,244 control chromosomes in the GnomAD database, including 51 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 0.020 (51 hom., cov: 32)
• Consequence: SAMD3 NM_001258275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

Genes affected

SAMD3 (HGNC:21574): (sterile alpha motif domain containing 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0195 (2973/152244) while in subpopulation AFR AF= 0.0448 (1862/41526). AF 95% confidence interval is 0.0431. There are 51 homozygotes in gnomad4. There are 1405 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD3	NM_001258275.3	c.-188+12877A>C		intron_variant
SAMD3	XM_024446335.2	c.-188+65019A>C		intron_variant
SAMD3	XM_047418239.1	c.-68+65019A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD3	ENST00000368134.6	c.-188+12877A>C		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0195 AC: 2970 AN: 152126 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00853

Gnomad OTH AF: 0.0205

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

GnomAD4 genome AF: 0.0195 AC: 2973 AN: 152244 Hom.: 51 Cov.: 32 AF XY: 0.0189 AC XY: 1405 AN XY: 74446

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.0135

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00472

Gnomad4 NFE AF: 0.00853

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0164 Hom.: 6

Bravo AF: 0.0219

Asia WGS AF: 0.00289 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.2
DANN	Benign	0.87

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: rs2169826; hg19: chr6-130621246;