rs4796995

Variant names:

• chr18-13708575-A-G
• rs4796995
• NM_152352.4:c.-29+17754T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-13708575-A-G
• chr18-13708575-A-T

Variant summary

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

The NM_152352.4(FAM210A):​c.-29+17754T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,048 control chromosomes in the GnomAD database, including 10,881 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 0.34 (10881 hom., cov: 32)
• Consequence: FAM210A NM_152352.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

FAM210A (HGNC:28346): (family with sequence similarity 210 member A) Predicted to be located in cytoplasm. Predicted to be active in mitochondrion. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM210A	NM_152352.4	c.-29+17754T>C		intron_variant	Intron 1 of 3	ENST00000651643.1	NP_689565.2
FAM210A	NM_001098801.2	c.-169+17754T>C		intron_variant	Intron 1 of 4		NP_001092271.1
FAM210A	XM_024451083.2	c.-29+16710T>C		intron_variant	Intron 1 of 3		XP_024306851.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM210A	ENST00000651643.1	c.-29+17754T>C		intron_variant	Intron 1 of 3		NM_152352.4	ENSP00000498370.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52055 AN: 151930 Hom.: 10858 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.343 AC: 52090 AN: 152048 Hom.: 10881 Cov.: 32 AF XY: 0.351 AC XY: 26124 AN XY: 74332

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.364

Alfa AF: 0.366 Hom.: 12584

Bravo AF: 0.347

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
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: rs4796995; hg19: chr18-13708574;