chr6-141202434-A-G

Variant names:

• chr6-141202434-A-G
• rs1869273

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 0.121 in 152,152 control chromosomes in the GnomAD database, including 2,092 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 0.12 (2092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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: 0.121 AC: 18401 AN: 152034 Hom.: 2084 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.121 AC: 18438 AN: 152152 Hom.: 2092 Cov.: 32 AF XY: 0.121 AC XY: 9028 AN XY: 74394

African (AFR) AF: 0.287 AC: 11925 AN: 41490

American (AMR) AF: 0.0608 AC: 929 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.178 AC: 915 AN: 5146

South Asian (SAS) AF: 0.183 AC: 886 AN: 4832

European-Finnish (FIN) AF: 0.0336 AC: 356 AN: 10610

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2619 AN: 68008

Other (OTH) AF: 0.124 AC: 262 AN: 2116

Alfa AF: 0.0927 Hom.: 211

Bravo AF: 0.128

Asia WGS AF: 0.208 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1869273; hg19: chr6-141523571;