chr6-35526822-C-T

Variant names:

• chr6-35526822-C-T
• rs1883637

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 0.0655 in 152,208 control chromosomes in the GnomAD database, including 477 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 0.066 (477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 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: 0.0656 AC: 9981 AN: 152090 Hom.: 476 Cov.: 31

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0655 AC: 9977 AN: 152208 Hom.: 477 Cov.: 31 AF XY: 0.0632 AC XY: 4702 AN XY: 74420

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.0612

Alfa AF: 0.0777 Hom.: 82

Bravo AF: 0.0702

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883637; hg19: chr6-35494599;