rs1883778

Positions:

• chr1-76993843-G-A
• chr1-76993843-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030965.3(ST6GALNAC5):​c.262-50361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,684 control chromosomes in the GnomAD database, including 10,915 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 0.34 (10915 hom., cov: 32)
• Consequence: ST6GALNAC5 NM_030965.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

ST6GALNAC5 (HGNC:19342): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5) The protein encoded by this gene is a Golgi type II transmembrane glycosyltransferase. The encoded protein catalyzes the transfer of sialic acid to cell surface proteins to modulate cell-cell interactions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GALNAC5	NM_030965.3	c.262-50361G>A		intron_variant		ENST00000477717.6	NP_112227.1
ST6GALNAC5	NM_001320273.2	c.262-56415G>A		intron_variant			NP_001307202.1
ST6GALNAC5	NM_001320274.2	c.262-69132G>A		intron_variant			NP_001307203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC5	ENST00000477717.6	c.262-50361G>A		intron_variant		1	NM_030965.3	ENSP00000417583	P1
ST6GALNAC5	ENST00000318803.6	c.262-50361G>A		intron_variant, NMD_transcript_variant		5		ENSP00000436263

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52102 AN: 151566 Hom.: 10912 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.344 AC: 52104 AN: 151684 Hom.: 10915 Cov.: 32 AF XY: 0.347 AC XY: 25699 AN XY: 74094

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.342

Alfa AF: 0.380 Hom.: 1869

Bravo AF: 0.316

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	12
DANN	Benign	0.39

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: rs1883778; hg19: chr1-77459528;