rs41288805

Variant names:

• chr2-27200457-G-A
• rs41288805
• NM_021095.4:c.1887C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-27200457-G-A
• chr2-27200457-G-C
• chr2-27200457-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_021095.4(SLC5A6):​c.1887C>T​(p.Ile629Ile) variant causes a synonymous 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: 32)
• Consequence: SLC5A6 NM_021095.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

SLC5A6 (HGNC:11041): (solute carrier family 5 member 6) Enables biotin transmembrane transporter activity and pantothenate transmembrane transporter activity. Involved in anion transmembrane transport and transport across blood-brain barrier. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP7: Synonymous conserved (PhyloP=-0.011 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A6	NM_021095.4	c.1887C>T	p.Ile629Ile	synonymous_variant	Exon 17 of 17	ENST00000310574.8	NP_066918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A6	ENST00000310574.8	c.1887C>T	p.Ile629Ile	synonymous_variant	Exon 17 of 17	1	NM_021095.4	ENSP00000310208.3
SLC5A6	ENST00000408041.5	c.1887C>T	p.Ile629Ile	synonymous_variant	Exon 18 of 18	1		ENSP00000384853.1
SLC5A6	ENST00000461757.1	n.1437C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
SLC5A6	ENST00000488743.6	n.2573C>T		non_coding_transcript_exon_variant	Exon 16 of 17	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	5.7
DANN	Benign	0.68

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: rs41288805; hg19: chr2-27423325; COSMIC: COSV104633807; COSMIC: COSV104633807;