chr4-67433907-A-C

Variant names:

• chr4-67433907-A-C
• rs1982973
• ENST00000502400.5:n.35-11907T>G

Variant summary

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

The ENST00000502400.5(ENSG00000250075):​n.35-11907T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,248 control chromosomes in the GnomAD database, including 3,872 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 0.22 (3872 hom., cov: 29)
• Consequence: ENSG00000250075 ENST00000502400.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 publications found

Genes affected

ENSG00000250075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502400.5. 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
	ENSG00000250075	ENST00000502400.5	TSL:2	n.35-11907T>G		intron	N/A
	ENSG00000250075	ENST00000652065.1		n.142-11907T>G		intron	N/A
	ENSG00000250075	ENST00000783862.1		n.128-11907T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33746 AN: 151128 Hom.: 3881 Cov.: 29

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.223 AC: 33730 AN: 151248 Hom.: 3872 Cov.: 29 AF XY: 0.228 AC XY: 16814 AN XY: 73824

African (AFR) AF: 0.165 AC: 6809 AN: 41152

American (AMR) AF: 0.180 AC: 2728 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3462

East Asian (EAS) AF: 0.217 AC: 1112 AN: 5114

South Asian (SAS) AF: 0.297 AC: 1412 AN: 4762

European-Finnish (FIN) AF: 0.323 AC: 3364 AN: 10420

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16770 AN: 67834

Other (OTH) AF: 0.208 AC: 437 AN: 2104

Alfa AF: 0.131 Hom.: 248

Bravo AF: 0.207

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.23
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1982973; hg19: chr4-68299625;