rs34623097

Variant names:

• chr5-148825046-G-A
• rs34623097
• ENST00000798472.1:n.255-130G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-148825046-G-A
• chr5-148825046-G-C

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.255-130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00714 in 152,336 control chromosomes in the GnomAD database, including 32 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 0.0071 (32 hom., cov: 33)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 4 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0814 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
ENSG00000303969	ENST00000798472.1	n.255-130G>A		intron_variant	Intron 2 of 4
ENSG00000303969	ENST00000798473.1	n.252-154G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.00714 AC: 1087 AN: 152216 Hom.: 32 Cov.: 33

Gnomad AFR AF: 0.000265

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00184

Gnomad OTH AF: 0.00478

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

GnomAD4 genome AF: 0.00714 AC: 1088 AN: 152336 Hom.: 32 Cov.: 33 AF XY: 0.00860 AC XY: 641 AN XY: 74502

African (AFR) AF: 0.000265 AC: 11 AN: 41576

American (AMR) AF: 0.00131 AC: 20 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3472

East Asian (EAS) AF: 0.0881 AC: 457 AN: 5190

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4830

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00184 AC: 125 AN: 68020

Other (OTH) AF: 0.00425 AC: 9 AN: 2116

Alfa AF: 0.00453 Hom.: 5

Bravo AF: 0.00503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.9
DANN	Benign	0.75
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs34623097; hg19: chr5-148204609;