chr1-200011644-T-C

Variant names:

• chr1-200011644-T-C
• rs6663479

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 0.0821 in 152,094 control chromosomes in the GnomAD database, including 572 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 0.082 (572 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0821 AC: 12470 AN: 151976 Hom.: 571 Cov.: 31

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0561

Gnomad EAS AF: 0.0145

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.0821 AC: 12484 AN: 152094 Hom.: 572 Cov.: 31 AF XY: 0.0789 AC XY: 5866 AN XY: 74386

African (AFR) AF: 0.0657 AC: 2729 AN: 41514

American (AMR) AF: 0.0711 AC: 1084 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0561 AC: 194 AN: 3460

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5176

South Asian (SAS) AF: 0.0585 AC: 282 AN: 4818

European-Finnish (FIN) AF: 0.0611 AC: 647 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7156 AN: 67970

Other (OTH) AF: 0.0859 AC: 181 AN: 2106

Alfa AF: 0.0919 Hom.: 243

Bravo AF: 0.0793

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.25
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6663479; hg19: chr1-199980772;