9-38718311-G-T

Variant summary

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

The NM_001394922.1(FAM240B):c.-4+1711C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,078 control chromosomes in the GnomAD database, including 11,611 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 0.37 (11611 hom., cov: 33)
• Consequence: FAM240B NM_001394922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32

Genes affected

FAM240B (HGNC:53430): (family with sequence similarity 240 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM240B	NM_001394922.1	c.-4+1711C>A		intron_variant		ENST00000637493.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM240B	ENST00000637493.2	c.-4+1711C>A		intron_variant		5	NM_001394922.1	P1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56557 AN: 151960 Hom.: 11577 Cov.: 33

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.372 AC: 56645 AN: 152078 Hom.: 11611 Cov.: 33 AF XY: 0.371 AC XY: 27576 AN XY: 74348

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.365

Alfa AF: 0.309 Hom.: 10327

Bravo AF: 0.372

Asia WGS AF: 0.494 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.014
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7848575; hg19: chr9-38718308;