chr20-56363408-A-G

Position:

• chr20-56363408-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080821.3(FAM210B):​c.187-1679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,106 control chromosomes in the GnomAD database, including 7,476 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 0.24 (7476 hom., cov: 32)
• Consequence: FAM210B NM_080821.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

FAM210B (HGNC:16102): (family with sequence similarity 210 member B) Involved in cellular response to estradiol stimulus and positive regulation of erythrocyte differentiation. Located in mitochondrial outer membrane. Is intrinsic component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM210B	NM_080821.3	c.187-1679A>G		intron_variant		ENST00000371384.4	NP_543011.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM210B	ENST00000371384.4	c.187-1679A>G		intron_variant		1	NM_080821.3	ENSP00000360437	P1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37196 AN: 151990 Hom.: 7455 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.245 AC: 37266 AN: 152106 Hom.: 7476 Cov.: 32 AF XY: 0.248 AC XY: 18426 AN XY: 74366

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.219

Alfa AF: 0.122 Hom.: 2792

Bravo AF: 0.271

Asia WGS AF: 0.430 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6024831; hg19: chr20-54938464;