chr6-78708525-A-G

Variant names:

• chr6-78708525-A-G
• rs1180809

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 0.208 in 152,120 control chromosomes in the GnomAD database, including 3,475 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 0.21 (3475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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: 0.209 AC: 31699 AN: 152002 Hom.: 3477 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.208 AC: 31701 AN: 152120 Hom.: 3475 Cov.: 32 AF XY: 0.211 AC XY: 15719 AN XY: 74346

African (AFR) AF: 0.192 AC: 7955 AN: 41504

American (AMR) AF: 0.211 AC: 3222 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3468

East Asian (EAS) AF: 0.157 AC: 813 AN: 5174

South Asian (SAS) AF: 0.132 AC: 635 AN: 4816

European-Finnish (FIN) AF: 0.283 AC: 2989 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14983 AN: 67986

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.115 Hom.: 195

Bravo AF: 0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1180809; hg19: chr6-79418242;