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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.217

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs237109; hg19: chr6-79414694;