chr6-83829706-G-A

Variant names:

• chr6-83829706-G-A
• rs1325474

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 0.241 in 152,068 control chromosomes in the GnomAD database, including 7,759 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 0.24 (7759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.240 AC: 36476 AN: 151950 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.241 AC: 36583 AN: 152068 Hom.: 7759 Cov.: 32 AF XY: 0.239 AC XY: 17811 AN XY: 74370

African (AFR) AF: 0.559 AC: 23143 AN: 41430

American (AMR) AF: 0.276 AC: 4213 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5166

South Asian (SAS) AF: 0.0692 AC: 334 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5484 AN: 67992

Other (OTH) AF: 0.195 AC: 411 AN: 2106

Alfa AF: 0.195 Hom.: 706

Bravo AF: 0.271

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1325474; hg19: chr6-84539425;