rs434468

Variant names:

• chr9-26382219-T-C
• rs434468
• ENST00000844068.1:n.628-35931A>G

Variant summary

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

The ENST00000844068.1(ENSG00000309811):​n.628-35931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,096 control chromosomes in the GnomAD database, including 4,216 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 (4216 hom., cov: 32)
• Consequence: ENSG00000309811 ENST00000844068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 0 publications found

Genes affected

ENSG00000309811 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375999	XR_001746565.1	n.372-35931A>G		intron_variant	Intron 3 of 3
LOC105375999	XR_001746566.2	n.342-35931A>G		intron_variant	Intron 3 of 3
LOC105375999	XR_001746567.1	n.464-35931A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309811	ENST00000844068.1	n.628-35931A>G		intron_variant	Intron 2 of 3
ENSG00000309811	ENST00000844069.1	n.213+41890A>G		intron_variant	Intron 2 of 2
ENSG00000309811	ENST00000844070.1	n.205-35931A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25973 AN: 151978 Hom.: 4209 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.171 AC: 26025 AN: 152096 Hom.: 4216 Cov.: 32 AF XY: 0.171 AC XY: 12706 AN XY: 74374

African (AFR) AF: 0.413 AC: 17133 AN: 41436

American (AMR) AF: 0.158 AC: 2415 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1252 AN: 5166

South Asian (SAS) AF: 0.197 AC: 949 AN: 4824

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10616

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0498 AC: 3388 AN: 67990

Other (OTH) AF: 0.148 AC: 311 AN: 2108

Alfa AF: 0.155 Hom.: 595

Bravo AF: 0.191

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.66
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs434468; hg19: chr9-26382217;