1-16059485-G-A

Position:

• chr1-16059485-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_182623.3(FAM131C):​c.562+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 1,599,760 control chromosomes in the GnomAD database, including 442,213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.69 (36818 hom., cov: 32)
  • Exomes 𝑓: 0.75 (405395 hom.)
• Consequence: FAM131C NM_182623.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.210

Genes affected

FAM131C (HGNC:26717): (family with sequence similarity 131 member C)

FAM131C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 1-16059485-G-A is Benign according to our data. Variant chr1-16059485-G-A is described in ClinVar as [Benign]. Clinvar id is 1287141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM131C	NM_182623.3	c.562+9C>T		intron_variant		ENST00000375662.5	NP_872429.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM131C	ENST00000375662.5	c.562+9C>T		intron_variant		1	NM_182623.3	ENSP00000364814.4
FAM131C	ENST00000494078.1	n.636+9C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104757 AN: 151232 Hom.: 36809 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.750

GnomAD3 exomes AF: 0.749 AC: 178717 AN: 238550 Hom.: 66641 AF XY: 0.752 AC XY: 97677 AN XY: 129884

Gnomad AFR exome AF: 0.494

Gnomad AMR exome AF: 0.850

Gnomad ASJ exome AF: 0.753

Gnomad EAS exome AF: 0.814

Gnomad SAS exome AF: 0.791

Gnomad FIN exome AF: 0.668

Gnomad NFE exome AF: 0.746

Gnomad OTH exome AF: 0.759

GnomAD4 exome AF: 0.749 AC: 1085014 AN: 1448412 Hom.: 405395 Cov.: 61 AF XY: 0.752 AC XY: 540786 AN XY: 719458

Gnomad4 AFR exome AF: 0.493

Gnomad4 AMR exome AF: 0.844

Gnomad4 ASJ exome AF: 0.756

Gnomad4 EAS exome AF: 0.833

Gnomad4 SAS exome AF: 0.804

Gnomad4 FIN exome AF: 0.676

Gnomad4 NFE exome AF: 0.749

Gnomad4 OTH exome AF: 0.745

GnomAD4 genome AF: 0.692 AC: 104804 AN: 151348 Hom.: 36818 Cov.: 32 AF XY: 0.694 AC XY: 51294 AN XY: 73916

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.750

Alfa AF: 0.717 Hom.: 9412

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 10, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.016
DANN	Benign	0.74

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: rs3884058; hg19: chr1-16385980; COSMIC: COSV65154015; COSMIC: COSV65154015;