chr1-200703778-G-T

Variant names:

• chr1-200703778-G-T
• rs7512898

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 0.551 in 152,080 control chromosomes in the GnomAD database, including 23,262 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 0.55 (23262 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 16 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 (AMR) allele frequency at 95% confidence interval = 0.595 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: 0.552 AC: 83816 AN: 151962 Hom.: 23266 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.551 AC: 83846 AN: 152080 Hom.: 23262 Cov.: 33 AF XY: 0.552 AC XY: 41019 AN XY: 74334

African (AFR) AF: 0.506 AC: 20998 AN: 41472

American (AMR) AF: 0.606 AC: 9254 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2809 AN: 5176

South Asian (SAS) AF: 0.557 AC: 2684 AN: 4816

European-Finnish (FIN) AF: 0.525 AC: 5531 AN: 10544

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38564 AN: 68004

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.562 Hom.: 46378

Bravo AF: 0.557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.41
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7512898; hg19: chr1-200672906;