rs237109

Variant names:

• chr6-78704977-T-A
• rs237109

Your query was ambiguous. Multiple possible variants found:

• chr6-78704977-T-A
• chr6-78704977-T-C

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 152,160 control chromosomes in the GnomAD database, including 3,496 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 (3496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31702 AN: 152042 Hom.: 3498 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.284

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: 31714 AN: 152160 Hom.: 3496 Cov.: 32 AF XY: 0.212 AC XY: 15746 AN XY: 74386

African (AFR) AF: 0.193 AC: 7996 AN: 41508

American (AMR) AF: 0.211 AC: 3219 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.156 AC: 809 AN: 5170

South Asian (SAS) AF: 0.133 AC: 642 AN: 4826

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10592

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

European-Non Finnish (NFE) AF: 0.220 AC: 14960 AN: 68002

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.125 Hom.: 209

Bravo AF: 0.203

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs237109; hg19: chr6-79414694;