chr4-99435861-G-A

Variant names:

• chr4-99435861-G-A
• rs2851028

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 0.86 in 153,630 control chromosomes in the GnomAD database, including 57,646 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 0.86 (57165 hom., cov: 32)
  • Exomes 𝑓: 0.82 (481 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 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: 0.861 AC: 130918 AN: 152108 Hom.: 57110 Cov.: 32

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.861

GnomAD4 exome AF: 0.825 AC: 1158 AN: 1404 Hom.: 481 AF XY: 0.824 AC XY: 577 AN XY: 700

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.823 AC: 232 AN: 282

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 19 AN: 38

South Asian (SAS) AF: 0.800 AC: 64 AN: 80

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.837 AC: 780 AN: 932

Other (OTH) AF: 0.879 AC: 58 AN: 66

GnomAD4 genome AF: 0.861 AC: 131030 AN: 152226 Hom.: 57165 Cov.: 32 AF XY: 0.859 AC XY: 63959 AN XY: 74424

African (AFR) AF: 0.969 AC: 40275 AN: 41566

American (AMR) AF: 0.812 AC: 12390 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2991 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2479 AN: 5168

South Asian (SAS) AF: 0.754 AC: 3637 AN: 4826

European-Finnish (FIN) AF: 0.886 AC: 9400 AN: 10608

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57024 AN: 68004

Other (OTH) AF: 0.860 AC: 1817 AN: 2112

Alfa AF: 0.852 Hom.: 93532

Bravo AF: 0.857

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.21
PhyloP100		0.34
PromoterAI		-0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2851028; hg19: chr4-100357018;