chr4-9765264-C-T

Variant names:

• chr4-9765264-C-T
• rs1878943

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 0.223 in 152,102 control chromosomes in the GnomAD database, including 4,050 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 (4050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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: 0.223 AC: 33952 AN: 151984 Hom.: 4039 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.179

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: 33980 AN: 152102 Hom.: 4050 Cov.: 33 AF XY: 0.225 AC XY: 16710 AN XY: 74352

African (AFR) AF: 0.288 AC: 11931 AN: 41480

American (AMR) AF: 0.236 AC: 3604 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3466

East Asian (EAS) AF: 0.322 AC: 1665 AN: 5164

South Asian (SAS) AF: 0.295 AC: 1424 AN: 4828

European-Finnish (FIN) AF: 0.173 AC: 1835 AN: 10584

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12148 AN: 67988

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.188 Hom.: 1859

Bravo AF: 0.231

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1878943; hg19: chr4-9766888;