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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.171 AC: 7110 AN: 41526

American (AMR) AF: 0.0197 AC: 300 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.0279 AC: 144 AN: 5170

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4820

European-Finnish (FIN) AF: 0.000472 AC: 5 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00481 AC: 327 AN: 67994

Other (OTH) AF: 0.0384 AC: 81 AN: 2112

Alfa AF: 0.0137 Hom.: 20

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10498983; hg19: chr6-93477038;