rs6663606

Positions:

• chr1-203295900-T-A
• chr1-203295900-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 0.401 in 151,822 control chromosomes in the GnomAD database, including 14,247 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 0.40 (14247 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60934 AN: 151704 Hom.: 14239 Cov.: 30

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.401 AC: 60946 AN: 151822 Hom.: 14247 Cov.: 30 AF XY: 0.405 AC XY: 30006 AN XY: 74156

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.439

Alfa AF: 0.459 Hom.: 2169

Bravo AF: 0.372

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.064
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6663606; hg19: chr1-203265028;