rs4760636

Variant names:

• chr12-47779569-T-A
• rs4760636
• NM_017842.3:c.304+374T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-47779569-T-A
• chr12-47779569-T-C
• chr12-47779569-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017842.3(SLC48A1):​c.304+374T>A 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: SLC48A1 NM_017842.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 15 publications found

Genes affected

SLC48A1 (HGNC:26035): (solute carrier family 48 member 1) Enables heme binding activity and heme transmembrane transporter activity. Involved in heme transport. Located in endosome membrane; lysosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017842.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC48A1	NM_017842.3	MANE Select	c.304+374T>A		intron	N/A	NP_060312.2	Q6P1K1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC48A1	ENST00000442218.3	TSL:1 MANE Select	c.304+374T>A		intron	N/A	ENSP00000415998.2	Q6P1K1-1
	SLC48A1	ENST00000442892.2	TSL:1	c.133+374T>A		intron	N/A	ENSP00000410134.2	Q6P1K1-2
	SLC48A1	ENST00000551301.1	TSL:2	n.*141+374T>A		intron	N/A	ENSP00000449036.1	F8VXV4

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.80
PhyloP100		-0.47

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: rs4760636; hg19: chr12-48173352;