chr4-98715064-A-G

Variant names:

• chr4-98715064-A-G
• rs17027976

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 0.14 in 152,212 control chromosomes in the GnomAD database, including 1,712 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 0.14 (1712 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 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: 0.140 AC: 21233 AN: 152094 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 152212 Hom.: 1712 Cov.: 32 AF XY: 0.145 AC XY: 10774 AN XY: 74406

African (AFR) AF: 0.171 AC: 7089 AN: 41530

American (AMR) AF: 0.172 AC: 2635 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.0616 AC: 319 AN: 5180

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4820

European-Finnish (FIN) AF: 0.175 AC: 1852 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7278 AN: 68006

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.114 Hom.: 1479

Bravo AF: 0.138

Asia WGS AF: 0.160 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.67
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs17027976; hg19: chr4-99636215;