4-27409438-A-G

Variant names:

• chr4-27409438-A-G
• rs1910137

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 0.398 in 151,878 control chromosomes in the GnomAD database, including 14,498 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 0.40 (14498 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.61
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60414 AN: 151760 Hom.: 14496 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.00831

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.398 AC: 60415 AN: 151878 Hom.: 14498 Cov.: 31 AF XY: 0.393 AC XY: 29149 AN XY: 74198

African (AFR) AF: 0.168 AC: 6967 AN: 41470

American (AMR) AF: 0.430 AC: 6537 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3470

East Asian (EAS) AF: 0.00833 AC: 43 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5610 AN: 10542

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36887 AN: 67884

Other (OTH) AF: 0.378 AC: 799 AN: 2114

Alfa AF: 0.485 Hom.: 3973

Bravo AF: 0.376

Asia WGS AF: 0.159 AC: 561 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs1910137; hg19: chr4-27411060;