rs6119625

Variant names:

• chr20-35572533-A-G
• rs6119625
• ENST00000611673.4:n.812+3634T>C

Variant summary

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

The ENST00000611673.4(ENSG00000293413):​n.812+3634T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,114 control chromosomes in the GnomAD database, including 2,357 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 0.17 (2357 hom., cov: 32)
• Consequence: ENSG00000293413 ENST00000611673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 15 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FER1L4	NR_119376.1	n.4393+3634T>C		intron_variant	Intron 35 of 42

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293413	ENST00000611673.4	n.812+3634T>C		intron_variant	Intron 8 of 14	2
ENSG00000293413	ENST00000613061.4	n.1216+3634T>C		intron_variant	Intron 9 of 15	5
FER1L4	ENST00000615531.4	n.4381+3634T>C		intron_variant	Intron 35 of 44	6

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25456 AN: 151996 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.167 AC: 25473 AN: 152114 Hom.: 2357 Cov.: 32 AF XY: 0.167 AC XY: 12434 AN XY: 74384

African (AFR) AF: 0.190 AC: 7893 AN: 41464

American (AMR) AF: 0.192 AC: 2936 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.145 AC: 752 AN: 5178

South Asian (SAS) AF: 0.284 AC: 1371 AN: 4822

European-Finnish (FIN) AF: 0.0921 AC: 976 AN: 10598

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10082 AN: 68002

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.175 Hom.: 659

Bravo AF: 0.172

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.39
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs6119625; hg19: chr20-34160455;