rs41515647

Positions:

• chr1-77051324-C-A
• chr1-77051324-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.86).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 168 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC5	NM_030965.3	c.779+959C>A		intron_variant		ENST00000477717.6
ST6GALNAC5	NM_001320273.2	c.*42+959C>A		intron_variant
ST6GALNAC5	NM_001320274.2	c.262-11651C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC5	ENST00000477717.6	c.779+959C>A		intron_variant		1	NM_030965.3	P1
ST6GALNAC5	ENST00000318803.6	c.*64+959C>A		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.00756

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0592

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

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: rs41515647; hg19: chr1-77517009;