rs10214237

Variant names:

• chr5-35883632-T-C
• rs10214237

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 0.213 in 152,168 control chromosomes in the GnomAD database, including 3,938 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 0.21 (3938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 28 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 (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.213 AC: 32351 AN: 152050 Hom.: 3940 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.213 AC: 32354 AN: 152168 Hom.: 3938 Cov.: 32 AF XY: 0.215 AC XY: 15975 AN XY: 74384

African (AFR) AF: 0.105 AC: 4346 AN: 41536

American (AMR) AF: 0.180 AC: 2748 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3472

East Asian (EAS) AF: 0.166 AC: 857 AN: 5178

South Asian (SAS) AF: 0.196 AC: 942 AN: 4812

European-Finnish (FIN) AF: 0.349 AC: 3694 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18221 AN: 67992

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.225 Hom.: 626

Bravo AF: 0.197

Asia WGS AF: 0.205 AC: 712 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	1.1
DANN	Benign	0.31
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10214237; hg19: chr5-35883734;