rs34037980

Variant names:

• chr2-203905331-A-G
• rs34037980
• ENST00000810800.1:n.203+8326A>G

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.203+8326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,226 control chromosomes in the GnomAD database, including 2,579 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 0.18 (2579 hom., cov: 33)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 12 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305408	ENST00000810800.1	n.203+8326A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27180 AN: 152108 Hom.: 2576 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.179 AC: 27194 AN: 152226 Hom.: 2579 Cov.: 33 AF XY: 0.177 AC XY: 13206 AN XY: 74426

African (AFR) AF: 0.118 AC: 4892 AN: 41554

American (AMR) AF: 0.194 AC: 2961 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.175 AC: 907 AN: 5190

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4822

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10582

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14123 AN: 67994

Other (OTH) AF: 0.209 AC: 441 AN: 2110

Alfa AF: 0.176 Hom.: 320

Bravo AF: 0.177

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs34037980; hg19: chr2-204770054;