4-10401921-T-C

Variant names:

• chr4-10401921-T-C
• rs11943276

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.206

Alfa AF: 0.217 Hom.: 829

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11943276; hg19: chr4-10403545;