chr1-104037935-A-G

Variant names:

• chr1-104037935-A-G
• rs1330402

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 0.256 in 151,332 control chromosomes in the GnomAD database, including 5,749 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 0.26 (5749 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.256 AC: 38701 AN: 151216 Hom.: 5750 Cov.: 30

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.256 AC: 38704 AN: 151332 Hom.: 5749 Cov.: 30 AF XY: 0.251 AC XY: 18544 AN XY: 73882

African (AFR) AF: 0.112 AC: 4651 AN: 41378

American (AMR) AF: 0.270 AC: 4082 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1035 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1066 AN: 5104

South Asian (SAS) AF: 0.153 AC: 733 AN: 4800

European-Finnish (FIN) AF: 0.274 AC: 2863 AN: 10456

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23249 AN: 67702

Other (OTH) AF: 0.283 AC: 595 AN: 2104

Alfa AF: 0.313 Hom.: 1988

Bravo AF: 0.252

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.56
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1330402; hg19: chr1-104580557;