chr4-4840609-G-A

Variant names:

• chr4-4840609-G-A
• rs41451149

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 0.137 in 152,146 control chromosomes in the GnomAD database, including 1,480 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 (1480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 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: 0.137 AC: 20879 AN: 152028 Hom.: 1476 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00656

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.137 AC: 20889 AN: 152146 Hom.: 1480 Cov.: 33 AF XY: 0.135 AC XY: 10021 AN XY: 74368

African (AFR) AF: 0.117 AC: 4848 AN: 41504

American (AMR) AF: 0.154 AC: 2360 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3468

East Asian (EAS) AF: 0.00658 AC: 34 AN: 5168

South Asian (SAS) AF: 0.163 AC: 786 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1359 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10447 AN: 67988

Other (OTH) AF: 0.142 AC: 299 AN: 2110

Alfa AF: 0.130 Hom.: 855

Bravo AF: 0.136

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs41451149; hg19: chr4-4842336;