rs2844538

Variant names:

• chr6-31381102-G-A
• rs2844538

Your query was ambiguous. Multiple possible variants found:

• chr6-31381102-G-A
• chr6-31381102-G-C
• chr6-31381102-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 0.606 in 151,718 control chromosomes in the GnomAD database, including 28,500 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 0.61 (28500 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

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 (SAS) allele frequency at 95% confidence interval = 0.643 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: 0.606 AC: 91840 AN: 151610 Hom.: 28472 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.606 AC: 91910 AN: 151718 Hom.: 28500 Cov.: 31 AF XY: 0.608 AC XY: 45055 AN XY: 74154

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.590

Alfa AF: 0.598 Hom.: 5555

Bravo AF: 0.591

Asia WGS AF: 0.605 AC: 2106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844538; hg19: chr6-31348879;