NM_030965.3:c.779+959C>A

Variant names:

• chr1-77051324-C-A
• rs41515647
• NM_030965.3:c.779+959C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_030965.3(ST6GALNAC5):​c.779+959C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,200 control chromosomes in the GnomAD database, including 168 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 0.044 (168 hom., cov: 32)
• Consequence: ST6GALNAC5 NM_030965.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 3 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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0438 (6670/152200) while in subpopulation NFE AF = 0.0501 (3409/68012). AF 95% confidence interval is 0.0487. There are 168 homozygotes in GnomAd4. There are 3162 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 168 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC5	NM_030965.3	c.779+959C>A		intron_variant	Intron 4 of 4	ENST00000477717.6	NP_112227.1
ST6GALNAC5	NM_001320273.2	c.*42+959C>A		intron_variant	Intron 3 of 3		NP_001307202.1
ST6GALNAC5	NM_001320274.2	c.262-11651C>A		intron_variant	Intron 2 of 2		NP_001307203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC5	ENST00000477717.6	c.779+959C>A		intron_variant	Intron 4 of 4	1	NM_030965.3	ENSP00000417583.1
ST6GALNAC5	ENST00000318803.6	n.*64+959C>A		intron_variant	Intron 4 of 4	5		ENSP00000436263.1

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6668 AN: 152082 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00754

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0599

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

GnomAD4 genome AF: 0.0438 AC: 6670 AN: 152200 Hom.: 168 Cov.: 32 AF XY: 0.0425 AC XY: 3162 AN XY: 74416

African (AFR) AF: 0.0397 AC: 1648 AN: 41524

American (AMR) AF: 0.0327 AC: 500 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3472

East Asian (EAS) AF: 0.00756 AC: 39 AN: 5162

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4822

European-Finnish (FIN) AF: 0.0298 AC: 316 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0501 AC: 3409 AN: 68012

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0234 Hom.: 10

Bravo AF: 0.0432

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-0.036
Mutation Taster		=100/0	polymorphism

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: rs41515647; hg19: chr1-77517009;