chr1-206861007-T-C

Variant names:

• chr1-206861007-T-C
• rs11808756

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 0.0547 in 152,254 control chromosomes in the GnomAD database, including 618 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 0.055 (618 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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: 0.0546 AC: 8313 AN: 152136 Hom.: 617 Cov.: 30

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0547 AC: 8322 AN: 152254 Hom.: 618 Cov.: 30 AF XY: 0.0526 AC XY: 3915 AN XY: 74450

African (AFR) AF: 0.164 AC: 6797 AN: 41514

American (AMR) AF: 0.0292 AC: 446 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5186

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4830

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00603 AC: 410 AN: 68020

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0351 Hom.: 47

Bravo AF: 0.0650

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.81
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs11808756; hg19: chr1-207034352;