chr1-150789695-C-T

Variant names:

• chr1-150789695-C-T
• rs10888395

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 0.354 in 152,082 control chromosomes in the GnomAD database, including 9,886 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 0.35 (9886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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: 0.354 AC: 53803 AN: 151964 Hom.: 9878 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.354 AC: 53823 AN: 152082 Hom.: 9886 Cov.: 32 AF XY: 0.359 AC XY: 26692 AN XY: 74340

African (AFR) AF: 0.277 AC: 11475 AN: 41484

American (AMR) AF: 0.419 AC: 6401 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1988 AN: 5160

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10570

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24922 AN: 67974

Other (OTH) AF: 0.370 AC: 781 AN: 2112

Alfa AF: 0.366 Hom.: 28051

Bravo AF: 0.349

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.56
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10888395; hg19: chr1-150762171;