rs6457614

Variant names:

• chr6-32684123-T-G
• rs6457614

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 0.132 in 151,240 control chromosomes in the GnomAD database, including 1,422 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 0.13 (1422 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 22 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 = 0.152 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: 0.132 AC: 19883 AN: 151118 Hom.: 1418 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.132 AC: 19911 AN: 151240 Hom.: 1422 Cov.: 33 AF XY: 0.134 AC XY: 9886 AN XY: 73896

African (AFR) AF: 0.155 AC: 6401 AN: 41272

American (AMR) AF: 0.116 AC: 1768 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 463 AN: 3434

East Asian (EAS) AF: 0.0466 AC: 238 AN: 5112

South Asian (SAS) AF: 0.0974 AC: 448 AN: 4600

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10582

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.116 AC: 7870 AN: 67758

Other (OTH) AF: 0.139 AC: 292 AN: 2098

Alfa AF: 0.124 Hom.: 582

Bravo AF: 0.125

Asia WGS AF: 0.103 AC: 362 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	11
DANN	Benign	0.62
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs6457614; hg19: chr6-32651900;