XR_002957397.2:n.245G>A

Variant names:

• chr12-6534163-C-T
• rs7971637
• XR_002957397.2:n.245G>A

Variant summary

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

The XR_002957397.2(GAPDH-DT):​n.245G>A 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 0.172 in 154,472 control chromosomes in the GnomAD database, including 2,504 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 0.17 (2469 hom., cov: 33)
  • Exomes 𝑓: 0.13 (35 hom.)
• Consequence: GAPDH-DT XR_002957397.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 12 publications found

Genes affected

GAPDH-DT (HGNC:55492): (GAPDH divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAPDH-DT	XR_002957397.2	n.245G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26325 AN: 152050 Hom.: 2472 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.135 AC: 310 AN: 2304 Hom.: 35 Cov.: 0 AF XY: 0.126 AC XY: 185 AN XY: 1472

African (AFR) AF: 0.167 AC: 2 AN: 12

American (AMR) AF: 0.134 AC: 22 AN: 164

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 1 AN: 10

East Asian (EAS) AF: 0.136 AC: 3 AN: 22

South Asian (SAS) AF: 0.0781 AC: 42 AN: 538

European-Finnish (FIN) AF: 0.192 AC: 10 AN: 52

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 12

European-Non Finnish (NFE) AF: 0.156 AC: 218 AN: 1400

Other (OTH) AF: 0.128 AC: 12 AN: 94

GnomAD4 genome AF: 0.173 AC: 26327 AN: 152168 Hom.: 2469 Cov.: 33 AF XY: 0.173 AC XY: 12865 AN XY: 74412

African (AFR) AF: 0.114 AC: 4743 AN: 41536

American (AMR) AF: 0.200 AC: 3066 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1585 AN: 5166

South Asian (SAS) AF: 0.123 AC: 594 AN: 4826

European-Finnish (FIN) AF: 0.207 AC: 2193 AN: 10600

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

European-Non Finnish (NFE) AF: 0.195 AC: 13259 AN: 67962

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.184 Hom.: 1406

Bravo AF: 0.173

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.92
PromoterAI		0.0074	Neutral
Mutation Taster		=300/0	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: rs7971637; hg19: chr12-6643329;