rs977096

Variant names:

• chr10-69630637-A-C
• rs977096
• NM_145306.3:c.-104+324A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-69630637-A-C
• chr10-69630637-A-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_145306.3(FAM241B):​c.-104+324A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000871 in 1,147,534 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 8.7e-7 (0 hom.)
• Consequence: FAM241B NM_145306.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 0 publications found

Genes affected

FAM241B (HGNC:23519): (family with sequence similarity 241 member B) Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM241B	NM_145306.3	c.-104+324A>C		intron_variant	Intron 1 of 3	ENST00000373279.6	NP_660349.1
FAM241B	XM_005269606.3	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 4		XP_005269663.1
FAM241B	XM_005269608.4	c.-36+324A>C		intron_variant	Intron 1 of 2		XP_005269665.1
FAM241B	XM_011539455.3	c.-742A>C		upstream_gene_variant			XP_011537757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM241B	ENST00000373279.6	c.-104+324A>C		intron_variant	Intron 1 of 3	1	NM_145306.3	ENSP00000362376.4
FAM241B	ENST00000421716.1	c.1A>C	p.Met1?	initiator_codon_variant	Exon 1 of 4	2		ENSP00000398621.1
FAM241B	ENST00000491890.1	n.63+324A>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.71e-7 AC: 1 AN: 1147534 Hom.: 0 Cov.: 32 AF XY: 0.00000178 AC XY: 1 AN XY: 562718

African (AFR) AF: 0.00 AC: 0 AN: 24258

American (AMR) AF: 0.00 AC: 0 AN: 27462

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15724

East Asian (EAS) AF: 0.00 AC: 0 AN: 12164

South Asian (SAS) AF: 0.00 AC: 0 AN: 75676

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27348

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4386

European-Non Finnish (NFE) AF: 0.00000109 AC: 1 AN: 919048

Other (OTH) AF: 0.00 AC: 0 AN: 41468

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	6.6
DANN	Benign	0.46
Eigen	Benign	-0.94
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.026	N
LIST_S2	Uncertain	0.90	D
MetaRNN	Uncertain	0.74	D
MetaSVM	Benign	-0.97	T
PhyloP100		0.11
PROVEAN	Benign	-0.33	N
REVEL	Benign	0.11
Sift	Pathogenic	0.0	D
MutPred		0.87		Loss of loop (P = 0.2237);
MVP		0.14
ClinPred		0.046	T
GERP RS		-4.2
PromoterAI		-0.12	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs977096; hg19: chr10-71390393;