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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634630.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283108	ENST00000634630.3	TSL:3	n.400+2326A>G		intron	N/A
	ENSG00000283108	ENST00000634951.1	TSL:3	n.206+2326A>G		intron	N/A
	ENSG00000283108	ENST00000773254.1		n.400+2326A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4804436;

hg19: chr19-9515200;