chr6-43242001-G-A

Variant names:

• chr6-43242001-G-A
• rs2104142

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 0.447 in 152,130 control chromosomes in the GnomAD database, including 16,382 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 0.45 (16382 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.447 AC: 67948 AN: 152012 Hom.: 16344 Cov.: 33

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.447 AC: 68057 AN: 152130 Hom.: 16382 Cov.: 33 AF XY: 0.442 AC XY: 32905 AN XY: 74362

African (AFR) AF: 0.641 AC: 26599 AN: 41482

American (AMR) AF: 0.408 AC: 6241 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1556 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2462 AN: 5178

South Asian (SAS) AF: 0.408 AC: 1971 AN: 4830

European-Finnish (FIN) AF: 0.327 AC: 3456 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24426 AN: 67990

Other (OTH) AF: 0.474 AC: 1001 AN: 2112

Alfa AF: 0.392 Hom.: 47271

Bravo AF: 0.462

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2104142; hg19: chr6-43209739;