rs2209544

Variant names:

• chr6-24157147-C-A
• rs2209544

Your query was ambiguous. Multiple possible variants found:

• chr6-24157147-C-A
• chr6-24157147-C-G
• chr6-24157147-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0839 in 152,164 control chromosomes in the GnomAD database, including 703 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 0.084 (703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 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: 0.0840 AC: 12765 AN: 152046 Hom.: 705 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0839 AC: 12767 AN: 152164 Hom.: 703 Cov.: 32 AF XY: 0.0853 AC XY: 6347 AN XY: 74390

African (AFR) AF: 0.0255 AC: 1058 AN: 41520

American (AMR) AF: 0.108 AC: 1648 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0553 AC: 192 AN: 3470

East Asian (EAS) AF: 0.170 AC: 880 AN: 5180

South Asian (SAS) AF: 0.140 AC: 676 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1189 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6874 AN: 67990

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0964 Hom.: 2481

Bravo AF: 0.0814

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.41
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2209544; hg19: chr6-24157375;