4-34984506-T-C

Variant names:

• chr4-34984506-T-C
• rs16990598

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 0.184 in 151,952 control chromosomes in the GnomAD database, including 2,864 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 0.18 (2864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 2 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.307 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: 0.183 AC: 27847 AN: 151836 Hom.: 2855 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 27891 AN: 151952 Hom.: 2864 Cov.: 32 AF XY: 0.185 AC XY: 13746 AN XY: 74282

African (AFR) AF: 0.263 AC: 10903 AN: 41440

American (AMR) AF: 0.180 AC: 2740 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5166

South Asian (SAS) AF: 0.166 AC: 799 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1262 AN: 10582

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9110 AN: 67910

Other (OTH) AF: 0.190 AC: 401 AN: 2108

Alfa AF: 0.148 Hom.: 956

Bravo AF: 0.195

Asia WGS AF: 0.231 AC: 805 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs16990598; hg19: chr4-34986128;