4-38784229-T-G

Variant names:

• chr4-38784229-T-G
• rs7663239

Variant summary

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

The variant allele was found at a frequency of 0.147 in 152,078 control chromosomes in the GnomAD database, including 2,850 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 0.15 (2850 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22360 AN: 151960 Hom.: 2831 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0871

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.147 AC: 22421 AN: 152078 Hom.: 2850 Cov.: 31 AF XY: 0.146 AC XY: 10849 AN XY: 74356

African (AFR) AF: 0.348 AC: 14390 AN: 41404

American (AMR) AF: 0.103 AC: 1577 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 449 AN: 5178

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4820

European-Finnish (FIN) AF: 0.0303 AC: 321 AN: 10610

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3799 AN: 67996

Other (OTH) AF: 0.174 AC: 367 AN: 2106

Alfa AF: 0.0848 Hom.: 4307

Bravo AF: 0.158

Asia WGS AF: 0.195 AC: 681 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	2.7
DANN	Benign	0.31
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7663239; hg19: chr4-38785850;