chr21-14495425-G-A

Variant names:

• chr21-14495425-G-A
• rs2822704
• NM_022136.5:c.919+3017C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_022136.5(SAMSN1):​c.919+3017C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 152,242 control chromosomes in the GnomAD database, including 646 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 0.053 (646 hom., cov: 33)
• Consequence: SAMSN1 NM_022136.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.37
• Publications: 0 publications found

Genes affected

SAMSN1 (HGNC:10528): (SAM domain, SH3 domain and nuclear localization signals 1) SAMSN1 is a member of a novel gene family of putative adaptors and scaffold proteins containing SH3 and SAM (sterile alpha motif) domains (Claudio et al., 2001 [PubMed 11536050]).[supplied by OMIM, Mar 2008]

LOC124905053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022136.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMSN1	NM_022136.5	MANE Select	c.919+3017C>T		intron	N/A	NP_071419.3
	SAMSN1	NM_001395858.1		c.1903+3017C>T		intron	N/A	NP_001382787.1
	SAMSN1	NM_001395857.1		c.1807+3017C>T		intron	N/A	NP_001382786.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMSN1	ENST00000400566.6	TSL:1 MANE Select	c.919+3017C>T		intron	N/A	ENSP00000383411.2
	SAMSN1	ENST00000285670.7	TSL:1	c.1123+3017C>T		intron	N/A	ENSP00000285670.2
	SAMSN1	ENST00000619120.4	TSL:1	c.712+3017C>T		intron	N/A	ENSP00000480850.1

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7973 AN: 152124 Hom.: 641 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.00384

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0526 AC: 8001 AN: 152242 Hom.: 646 Cov.: 33 AF XY: 0.0510 AC XY: 3797 AN XY: 74446

African (AFR) AF: 0.170 AC: 7051 AN: 41522

American (AMR) AF: 0.0264 AC: 404 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4826

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.00384 AC: 261 AN: 68018

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0341 Hom.: 200

Bravo AF: 0.0597

Asia WGS AF: 0.0140 AC: 49 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	21
DANN	Benign	0.66
PhyloP100		3.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2822704; hg19: chr21-15867746;