2-84040305-A-G

Variant names:

• chr2-84040305-A-G
• rs2238
• ENST00000451049.1:n.416T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451049.1(ST6GALNAC2P1):​n.416T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,296 control chromosomes in the GnomAD database, including 60,783 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 0.89 (60744 hom., cov: 32)
  • Exomes 𝑓: 0.88 (39 hom.)
• Consequence: ST6GALNAC2P1 ENST00000451049.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 5 publications found

Genes affected

ST6GALNAC2P1 (HGNC:45160): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC2P1		n.84040305A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC2P1	ENST00000451049.1	n.416T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135515 AN: 152080 Hom.: 60685 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.882

GnomAD4 exome AF: 0.878 AC: 86 AN: 98 Hom.: 39 Cov.: 0 AF XY: 0.846 AC XY: 66 AN XY: 78

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.857 AC: 72 AN: 84

Other (OTH) AF: 1.00 AC: 6 AN: 6

GnomAD4 genome AF: 0.891 AC: 135632 AN: 152198 Hom.: 60744 Cov.: 32 AF XY: 0.893 AC XY: 66490 AN XY: 74426

African (AFR) AF: 0.972 AC: 40370 AN: 41546

American (AMR) AF: 0.905 AC: 13839 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3048 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5157 AN: 5160

South Asian (SAS) AF: 0.954 AC: 4602 AN: 4826

European-Finnish (FIN) AF: 0.853 AC: 9047 AN: 10600

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56854 AN: 67982

Other (OTH) AF: 0.884 AC: 1870 AN: 2116

Alfa AF: 0.854 Hom.: 65180

Bravo AF: 0.896

Asia WGS AF: 0.972 AC: 3380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.44
PhyloP100		-0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2238; hg19: chr2-84267429;