2-238971222-C-T

Variant names:

• chr2-238971222-C-T
• rs6543544

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 0.443 in 152,082 control chromosomes in the GnomAD database, including 15,208 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 0.44 (15208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 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: 0.443 AC: 67292 AN: 151964 Hom.: 15182 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.443 AC: 67360 AN: 152082 Hom.: 15208 Cov.: 32 AF XY: 0.436 AC XY: 32413 AN XY: 74340

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.458

Alfa AF: 0.466 Hom.: 16738

Bravo AF: 0.443

Asia WGS AF: 0.363 AC: 1266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6543544; hg19: chr2-239892918;