chr6-39149922-T-G

Variant names:

• chr6-39149922-T-G
• rs2115200

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 0.169 in 152,100 control chromosomes in the GnomAD database, including 2,623 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 0.17 (2623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.241 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: 0.169 AC: 25748 AN: 151982 Hom.: 2621 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.169 AC: 25749 AN: 152100 Hom.: 2623 Cov.: 32 AF XY: 0.169 AC XY: 12559 AN XY: 74344

African (AFR) AF: 0.0410 AC: 1705 AN: 41538

American (AMR) AF: 0.192 AC: 2928 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.173 AC: 894 AN: 5166

South Asian (SAS) AF: 0.253 AC: 1214 AN: 4800

European-Finnish (FIN) AF: 0.192 AC: 2031 AN: 10570

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15484 AN: 67960

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.188 Hom.: 2382

Bravo AF: 0.164

Asia WGS AF: 0.211 AC: 735 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	1.8
DANN	Benign	0.50
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs2115200; hg19: chr6-39117698;