chr1-74988307-G-A

Variant names:

• chr1-74988307-G-A
• rs113528169

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 0.144 in 152,232 control chromosomes in the GnomAD database, including 1,924 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 0.14 (1924 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 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: 0.144 AC: 21849 AN: 152114 Hom.: 1922 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.144 AC: 21855 AN: 152232 Hom.: 1924 Cov.: 32 AF XY: 0.147 AC XY: 10924 AN XY: 74428

African (AFR) AF: 0.0504 AC: 2097 AN: 41566

American (AMR) AF: 0.225 AC: 3439 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3468

East Asian (EAS) AF: 0.137 AC: 706 AN: 5170

South Asian (SAS) AF: 0.316 AC: 1528 AN: 4832

European-Finnish (FIN) AF: 0.153 AC: 1618 AN: 10598

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11571 AN: 68006

Other (OTH) AF: 0.141 AC: 299 AN: 2116

Alfa AF: 0.149 Hom.: 236

Bravo AF: 0.141

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs113528169; hg19: chr1-75453991;