rs4804436

Variant names:

• chr19-9404524-T-C
• rs4804436
• ENST00000634630.3:n.400+2326A>G

Variant summary

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

The ENST00000634630.3(ENSG00000283108):​n.400+2326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,694 control chromosomes in the GnomAD database, including 24,676 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 0.57 (24676 hom., cov: 30)
• Consequence: ENSG00000283108 ENST00000634630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 15 publications found

Genes affected

ENSG00000283108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268250	XR_002958434.2	n.211+2326A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283108	ENST00000634630.3	n.400+2326A>G		intron_variant	Intron 1 of 1	3
ENSG00000283108	ENST00000634951.1	n.206+2326A>G		intron_variant	Intron 1 of 2	3
ENSG00000283108	ENST00000773254.1	n.400+2326A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86053 AN: 151576 Hom.: 24661 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.568 AC: 86112 AN: 151694 Hom.: 24676 Cov.: 30 AF XY: 0.561 AC XY: 41603 AN XY: 74112

African (AFR) AF: 0.604 AC: 24957 AN: 41350

American (AMR) AF: 0.531 AC: 8097 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2264 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2099 AN: 5132

South Asian (SAS) AF: 0.573 AC: 2749 AN: 4800

European-Finnish (FIN) AF: 0.445 AC: 4660 AN: 10482

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39452 AN: 67918

Other (OTH) AF: 0.587 AC: 1233 AN: 2100

Alfa AF: 0.573 Hom.: 3609

Bravo AF: 0.575

Asia WGS AF: 0.507 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4804436; hg19: chr19-9515200;