rs1209912

Positions:

• chr21-38777718-G-A
• chr21-38777718-G-T

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 0.551 in 152,004 control chromosomes in the GnomAD database, including 26,926 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 0.55 (26926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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: 0.552 AC: 83768 AN: 151884 Hom.: 26930 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.551 AC: 83769 AN: 152004 Hom.: 26926 Cov.: 32 AF XY: 0.556 AC XY: 41296 AN XY: 74318

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.564

Alfa AF: 0.622 Hom.: 4244

Bravo AF: 0.529

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1209912; hg19: chr21-40149642;