chr4-99335572-C-G

Variant names:

• chr4-99335572-C-G
• rs1789895

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 0.233 in 152,080 control chromosomes in the GnomAD database, including 4,897 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 0.23 (4897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.233 AC: 35390 AN: 151962 Hom.: 4894 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35403 AN: 152080 Hom.: 4897 Cov.: 32 AF XY: 0.231 AC XY: 17171 AN XY: 74326

African (AFR) AF: 0.117 AC: 4845 AN: 41522

American (AMR) AF: 0.198 AC: 3027 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3468

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5170

South Asian (SAS) AF: 0.195 AC: 941 AN: 4816

European-Finnish (FIN) AF: 0.371 AC: 3908 AN: 10546

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21125 AN: 67958

Other (OTH) AF: 0.207 AC: 437 AN: 2108

Alfa AF: 0.279 Hom.: 817

Bravo AF: 0.213

Asia WGS AF: 0.114 AC: 395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs1789895; hg19: chr4-100256729;