20-35583402-G-A

Variant names:

• chr20-35583402-G-A
• rs6088887
• ENST00000430275.6:n.2948-140C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611673.4(ENSG00000293413):​n.414-6574C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 372,570 control chromosomes in the GnomAD database, including 8,173 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 0.19 (2990 hom., cov: 32)
  • Exomes 𝑓: 0.21 (5183 hom.)
• Consequence: ENSG00000293413 ENST00000611673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 26 publications found

Genes affected

ENSG00000293413 (HGNC:):

FER1L4 (HGNC:15801): (fer-1 like family member 4 (pseudogene)) Predicted to enable metal ion binding activity. Predicted to be involved in plasma membrane organization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611673.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FER1L4	NR_119376.1		n.3073-140C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293413	ENST00000430275.6	TSL:5	n.2948-140C>T		intron	N/A
	ENSG00000293413	ENST00000611673.4	TSL:2	n.414-6574C>T		intron	N/A
	FER1L4	ENST00000615531.4	TSL:6	n.3005-140C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29005 AN: 151828 Hom.: 2989 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.205 AC: 45279 AN: 220624 Hom.: 5183 AF XY: 0.216 AC XY: 26354 AN XY: 122234

African (AFR) AF: 0.195 AC: 1160 AN: 5962

American (AMR) AF: 0.159 AC: 2452 AN: 15402

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1532 AN: 5220

East Asian (EAS) AF: 0.0847 AC: 716 AN: 8456

South Asian (SAS) AF: 0.281 AC: 12989 AN: 46196

European-Finnish (FIN) AF: 0.141 AC: 1317 AN: 9360

Middle Eastern (MID) AF: 0.325 AC: 576 AN: 1774

European-Non Finnish (NFE) AF: 0.190 AC: 22405 AN: 117794

Other (OTH) AF: 0.204 AC: 2132 AN: 10460

GnomAD4 genome AF: 0.191 AC: 29008 AN: 151946 Hom.: 2990 Cov.: 32 AF XY: 0.189 AC XY: 14030 AN XY: 74282

African (AFR) AF: 0.192 AC: 7979 AN: 41450

American (AMR) AF: 0.187 AC: 2853 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3468

East Asian (EAS) AF: 0.0908 AC: 465 AN: 5120

South Asian (SAS) AF: 0.286 AC: 1374 AN: 4798

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10594

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13097 AN: 67940

Other (OTH) AF: 0.219 AC: 462 AN: 2108

Alfa AF: 0.195 Hom.: 12214

Bravo AF: 0.190

Asia WGS AF: 0.203 AC: 705 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.86
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6088887; hg19: chr20-34171324;