rs10516343

Positions:

• chr4-19973239-C-A
• chr4-19973239-C-G

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 0.802 in 152,198 control chromosomes in the GnomAD database, including 49,168 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 0.80 (49168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121915 AN: 152080 Hom.: 49118 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.802 AC: 122023 AN: 152198 Hom.: 49168 Cov.: 32 AF XY: 0.803 AC XY: 59718 AN XY: 74394

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.815

Alfa AF: 0.775 Hom.: 77847

Bravo AF: 0.807

Asia WGS AF: 0.790 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516343; hg19: chr4-19974862;