rs10499649

Variant names:

• chr7-46368772-C-G
• rs10499649

Your query was ambiguous. Multiple possible variants found:

• chr7-46368772-C-G
• chr7-46368772-C-T

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 0.0725 in 152,134 control chromosomes in the GnomAD database, including 920 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 0.072 (920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 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: 0.0723 AC: 10985 AN: 152016 Hom.: 908 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.000471

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00726

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0725 AC: 11029 AN: 152134 Hom.: 920 Cov.: 32 AF XY: 0.0719 AC XY: 5348 AN XY: 74374

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.000471

Gnomad4 NFE AF: 0.00726

Gnomad4 OTH AF: 0.0606

Alfa AF: 0.00240 Hom.: 3

Bravo AF: 0.0862

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499649; hg19: chr7-46408370;