rs1175550

Variant names:

• chr1-3774964-A-C
• NM_001288583.2:c.-75-335A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-3774964-A-C
• chr1-3774964-A-G
• chr1-3774964-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001288583.2(SMIM1):​c.-75-335A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: SMIM1 NM_001288583.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.55

Genes affected

SMIM1 (HGNC:44204): (small integral membrane protein 1 (Vel blood group)) This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM1	NM_001288583.2	c.-75-335A>C		intron_variant	Intron 2 of 3	ENST00000642557.4	NP_001275512.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM1	ENST00000642557.4	c.-75-335A>C		intron_variant	Intron 2 of 3		NM_001288583.2	ENSP00000496314.2
SMIM1	ENST00000444870.7	c.-75-335A>C		intron_variant	Intron 2 of 3	1		ENSP00000457386.1
SMIM1	ENST00000561886.2	c.-75-335A>C		intron_variant	Intron 2 of 2	2		ENSP00000456559.1
SMIM1	ENST00000452264.1	c.-75-335A>C		intron_variant	Intron 1 of 1	2		ENSP00000457674.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.44

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-3691528;