rs17287770

Variant names:

• chr3-46612935-C-G
• rs17287770
• NM_001195442.2:c.15+237C>G

Variant summary

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

The NM_001195442.2(FAM240A):​c.15+237C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,228 control chromosomes in the GnomAD database, including 209 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 0.046 (209 hom., cov: 32)
• Consequence: FAM240A NM_001195442.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 1 publications found

Genes affected

FAM240A (HGNC:52390): (family with sequence similarity 240 member A)

ENSG00000283877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM240A	NM_001195442.2	c.15+237C>G		intron_variant	Intron 1 of 2	ENST00000640551.3	NP_001182371.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM240A	ENST00000640551.3	c.15+237C>G		intron_variant	Intron 1 of 2	2	NM_001195442.2	ENSP00000491838.2
ENSG00000283877	ENST00000505797.1	n.*195-4248C>G		intron_variant	Intron 3 of 3	3		ENSP00000490854.1

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6974 AN: 152110 Hom.: 209 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0458 AC: 6972 AN: 152228 Hom.: 209 Cov.: 32 AF XY: 0.0437 AC XY: 3252 AN XY: 74426

African (AFR) AF: 0.0139 AC: 578 AN: 41528

American (AMR) AF: 0.0407 AC: 622 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4818

European-Finnish (FIN) AF: 0.0566 AC: 601 AN: 10612

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0694 AC: 4723 AN: 68010

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0581 Hom.: 34

Bravo AF: 0.0435

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		0.31
PromoterAI		-0.0082	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17287770; hg19: chr3-46654425;