rs10498983

Variant names:

• chr6-92767320-G-A
• rs10498983

Your query was ambiguous. Multiple possible variants found:

• chr6-92767320-G-A
• chr6-92767320-G-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 0.054 in 152,164 control chromosomes in the GnomAD database, including 616 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 0.054 (616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.0538 AC: 8187 AN: 152046 Hom.: 614 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0197

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.000472

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00481

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0540 AC: 8213 AN: 152164 Hom.: 616 Cov.: 32 AF XY: 0.0531 AC XY: 3952 AN XY: 74392

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.0279

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.000472

Gnomad4 NFE AF: 0.00481

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.00907 Hom.: 14

Bravo AF: 0.0593

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.36
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498983; hg19: chr6-93477038;