chr1-35208710-A-G

Variant names:

• chr1-35208710-A-G
• rs7543044

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 0.249 in 151,830 control chromosomes in the GnomAD database, including 7,912 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 0.25 (7912 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.249 AC: 37702 AN: 151712 Hom.: 7874 Cov.: 29

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.249 AC: 37805 AN: 151830 Hom.: 7912 Cov.: 29 AF XY: 0.250 AC XY: 18585 AN XY: 74196

African (AFR) AF: 0.543 AC: 22424 AN: 41332

American (AMR) AF: 0.285 AC: 4338 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 380 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2635 AN: 5126

South Asian (SAS) AF: 0.185 AC: 892 AN: 4812

European-Finnish (FIN) AF: 0.0894 AC: 947 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0835 AC: 5676 AN: 67970

Other (OTH) AF: 0.226 AC: 476 AN: 2110

Alfa AF: 0.125 Hom.: 6899

Bravo AF: 0.279

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs7543044; hg19: chr1-35674311;