1-107003753-A-G

Variant names:

• chr1-107003753-A-G
• rs17496332

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 0.261 in 152,040 control chromosomes in the GnomAD database, including 5,939 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 (5939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.261 AC: 39683 AN: 151924 Hom.: 5933 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.261 AC: 39695 AN: 152040 Hom.: 5939 Cov.: 32 AF XY: 0.260 AC XY: 19292 AN XY: 74320

African (AFR) AF: 0.108 AC: 4487 AN: 41484

American (AMR) AF: 0.255 AC: 3888 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1553 AN: 5156

South Asian (SAS) AF: 0.314 AC: 1511 AN: 4816

European-Finnish (FIN) AF: 0.299 AC: 3164 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23031 AN: 67968

Other (OTH) AF: 0.254 AC: 537 AN: 2116

Alfa AF: 0.311 Hom.: 22457

Bravo AF: 0.249

Asia WGS AF: 0.311 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs17496332; hg19: chr1-107546375; COSMIC: COSV59987475;