chr6-42527540-T-C

Variant names:

• chr6-42527540-T-C
• rs16895812

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 0.204 in 152,106 control chromosomes in the GnomAD database, including 3,176 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 0.20 (3176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31025 AN: 151988 Hom.: 3169 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.204 AC: 31045 AN: 152106 Hom.: 3176 Cov.: 32 AF XY: 0.202 AC XY: 14993 AN XY: 74370

African (AFR) AF: 0.210 AC: 8692 AN: 41468

American (AMR) AF: 0.178 AC: 2712 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.153 AC: 792 AN: 5178

South Asian (SAS) AF: 0.199 AC: 959 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2330 AN: 10572

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14251 AN: 68010

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.207 Hom.: 11861

Bravo AF: 0.201

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs16895812; hg19: chr6-42495278;