4-80263187-A-T

Variant names:

• chr4-80263187-A-T
• rs16998073

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 0.242 in 152,016 control chromosomes in the GnomAD database, including 5,081 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 0.24 (5081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 120 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.242 AC: 36742 AN: 151898 Hom.: 5085 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.242 AC: 36736 AN: 152016 Hom.: 5081 Cov.: 32 AF XY: 0.242 AC XY: 17979 AN XY: 74306

African (AFR) AF: 0.113 AC: 4668 AN: 41486

American (AMR) AF: 0.263 AC: 4023 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 799 AN: 3464

East Asian (EAS) AF: 0.380 AC: 1958 AN: 5146

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4808

European-Finnish (FIN) AF: 0.280 AC: 2960 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20014 AN: 67940

Other (OTH) AF: 0.238 AC: 503 AN: 2114

Alfa AF: 0.264 Hom.: 3046

Bravo AF: 0.235

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.8
DANN	Benign	0.82
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs16998073; hg19: chr4-81184341;