chr4-10401921-T-C

Variant names:

• chr4-10401921-T-C
• rs11943276

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 0.201 in 152,112 control chromosomes in the GnomAD database, including 3,265 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 0.20 (3265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.251 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: 0.201 AC: 30604 AN: 151994 Hom.: 3261 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.201 AC: 30617 AN: 152112 Hom.: 3265 Cov.: 32 AF XY: 0.201 AC XY: 14945 AN XY: 74348

African (AFR) AF: 0.142 AC: 5905 AN: 41484

American (AMR) AF: 0.257 AC: 3930 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3470

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5180

South Asian (SAS) AF: 0.180 AC: 867 AN: 4822

European-Finnish (FIN) AF: 0.206 AC: 2184 AN: 10584

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15732 AN: 67984

Other (OTH) AF: 0.206 AC: 436 AN: 2112

Alfa AF: 0.217 Hom.: 5378

Bravo AF: 0.204

Asia WGS AF: 0.111 AC: 387 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	0.71
DANN	Benign	0.54
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11943276; hg19: chr4-10403545;