1-76930481-T-C

Position:

• chr1-76930481-T-C

Variant summary

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

The NM_030965.3(ST6GALNAC5):​c.261+61739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,990 control chromosomes in the GnomAD database, including 9,701 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 0.32 (9701 hom., cov: 32)
• Consequence: ST6GALNAC5 NM_030965.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC5	NM_030965.3	c.261+61739T>C		intron_variant		ENST00000477717.6
ST6GALNAC5	NM_001320273.2	c.261+61739T>C		intron_variant
ST6GALNAC5	NM_001320274.2	c.261+61739T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC5	ENST00000477717.6	c.261+61739T>C		intron_variant		1	NM_030965.3	P1
ST6GALNAC5	ENST00000318803.6	c.261+61739T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49029 AN: 151872 Hom.: 9698 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.323 AC: 49040 AN: 151990 Hom.: 9701 Cov.: 32 AF XY: 0.323 AC XY: 24017 AN XY: 74302

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.317

Alfa AF: 0.404 Hom.: 21311

Bravo AF: 0.300

Asia WGS AF: 0.309 AC: 1074 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.67

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: rs17368584; hg19: chr1-77396166;