chr1-76930481-T-C

Variant names:

• chr1-76930481-T-C
• rs17368584
• NM_030965.3:c.261+61739T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030965.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC5	NM_030965.3	MANE Select	c.261+61739T>C		intron	N/A	NP_112227.1
	ST6GALNAC5	NM_001320273.2		c.261+61739T>C		intron	N/A	NP_001307202.1
	ST6GALNAC5	NM_001320274.2		c.261+61739T>C		intron	N/A	NP_001307203.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC5	ENST00000477717.6	TSL:1 MANE Select	c.261+61739T>C		intron	N/A	ENSP00000417583.1
	ST6GALNAC5	ENST00000318803.6	TSL:5	n.261+61739T>C		intron	N/A	ENSP00000436263.1

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

African (AFR) AF: 0.0963 AC: 4001 AN: 41532

American (AMR) AF: 0.350 AC: 5345 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1352 AN: 5138

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4816

European-Finnish (FIN) AF: 0.493 AC: 5194 AN: 10546

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29612 AN: 67930

Other (OTH) AF: 0.317 AC: 667 AN: 2106

Alfa AF: 0.383 Hom.: 32562

Bravo AF: 0.300

Asia WGS AF: 0.309 AC: 1074 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.67
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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: rs17368584; hg19: chr1-77396166;