rs10518221

Variant names:

• chr4-79649346-T-C
• rs10518221

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 0.113 in 152,168 control chromosomes in the GnomAD database, including 1,113 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 0.11 (1113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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: 0.113 AC: 17182 AN: 152050 Hom.: 1114 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.113 AC: 17184 AN: 152168 Hom.: 1113 Cov.: 32 AF XY: 0.110 AC XY: 8211 AN XY: 74388

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.128

Alfa AF: 0.112 Hom.: 1413

Bravo AF: 0.117

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
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: rs10518221; hg19: chr4-80570500;