chr21-42304243-G-A

Position:

• chr21-42304243-G-A

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 0.618 in 152,000 control chromosomes in the GnomAD database, including 29,090 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 0.62 (29090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 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: 0.618 AC: 93861 AN: 151882 Hom.: 29072 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.618 AC: 93931 AN: 152000 Hom.: 29090 Cov.: 32 AF XY: 0.620 AC XY: 46060 AN XY: 74302

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.614

Alfa AF: 0.618 Hom.: 40073

Bravo AF: 0.612

Asia WGS AF: 0.547 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs15661; hg19: chr21-43724353;