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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451049.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC2P1	ENST00000451049.1	TSL:6	n.416T>C		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2238;

hg19: chr2-84267429;