1-216459318-A-G

Variant names:

• chr1-216459318-A-G
• rs10495023

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 0.436 in 152,100 control chromosomes in the GnomAD database, including 14,518 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 0.44 (14518 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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: 0.436 AC: 66256 AN: 151982 Hom.: 14513 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.436 AC: 66306 AN: 152100 Hom.: 14518 Cov.: 33 AF XY: 0.436 AC XY: 32449 AN XY: 74342

African (AFR) AF: 0.453 AC: 18775 AN: 41480

American (AMR) AF: 0.442 AC: 6747 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2171 AN: 5168

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4820

European-Finnish (FIN) AF: 0.419 AC: 4429 AN: 10568

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29576 AN: 68004

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.437 Hom.: 2929

Bravo AF: 0.439

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.0
DANN	Benign	0.82
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10495023; hg19: chr1-216632660; COSMIC: COSV107160379;