rs1868751

Variant names:

• chr10-59346228-T-C
• rs1868751
• NM_198215.4:c.324+6042A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-59346228-T-C
• chr10-59346228-T-G

Variant summary

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

The NM_198215.4(FAM13C):​c.324+6042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,168 control chromosomes in the GnomAD database, including 2,222 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 0.16 (2222 hom., cov: 33)
• Consequence: FAM13C NM_198215.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 0 publications found

Genes affected

FAM13C (HGNC:19371): (family with sequence similarity 13 member C)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM13C	NM_198215.4	c.324+6042A>G		intron_variant	Intron 3 of 13	ENST00000618804.5	NP_937858.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM13C	ENST00000618804.5	c.324+6042A>G		intron_variant	Intron 3 of 13	1	NM_198215.4	ENSP00000481854.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24343 AN: 152050 Hom.: 2221 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.160 AC: 24355 AN: 152168 Hom.: 2222 Cov.: 33 AF XY: 0.159 AC XY: 11817 AN XY: 74410

African (AFR) AF: 0.214 AC: 8894 AN: 41490

American (AMR) AF: 0.123 AC: 1888 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3472

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5168

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4824

European-Finnish (FIN) AF: 0.0963 AC: 1022 AN: 10608

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8763 AN: 68006

Other (OTH) AF: 0.164 AC: 346 AN: 2106

Alfa AF: 0.0622 Hom.: 63

Bravo AF: 0.166

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.58
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1868751; hg19: chr10-61105988;