rs71018020

Variant names:

• chr6-87477166-GGTGTGTGTGT-G
• rs71018020
• NM_006416.5:c.17-180_17-171delTGTGTGTGTG

Your query was ambiguous. Multiple possible variants found:

• chr6-87477166-GGTGTGTGTGT-G
• chr6-87477166-GGTGTGTGTGT-GGT
• chr6-87477166-GGTGTGTGTGT-GGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006416.5(SLC35A1):​c.17-180_17-171delTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0090 (8 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905

Genes affected

SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

ENSG00000213204 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-180_17-171delTGTGTGTGTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-180_17-171delTGTGTGTGTG		intron_variant	Intron 1 of 6		NP_001161870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-195_17-186delGTGTGTGTGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-195_*61-186delGTGTGTGTGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00899 AC: 1346 AN: 149768 Hom.: 8 Cov.: 0

Gnomad AFR AF: 0.00263

Gnomad AMI AF: 0.0574

Gnomad AMR AF: 0.00560

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.000391

Gnomad SAS AF: 0.00588

Gnomad FIN AF: 0.00419

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.00585

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

GnomAD4 genome AF: 0.00898 AC: 1346 AN: 149872 Hom.: 8 Cov.: 0 AF XY: 0.00849 AC XY: 620 AN XY: 73036

Gnomad4 AFR AF: 0.00262

Gnomad4 AMR AF: 0.00560

Gnomad4 ASJ AF: 0.0151

Gnomad4 EAS AF: 0.000392

Gnomad4 SAS AF: 0.00589

Gnomad4 FIN AF: 0.00419

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.00580

Alfa AF: 0.00453 Hom.: 299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71018020; hg19: chr6-88186884;