2-241897239-G-A

Variant names:

• chr2-241897239-G-A
• rs757669825
• NM_001382368.1:c.108C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001382368.1(FAM240C):​c.108C>T​(p.His36His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000429 in 1,397,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000043 (0 hom.)
• Consequence: FAM240C NM_001382368.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.50
• Publications: 0 publications found

Genes affected

FAM240C (HGNC:54200): (family with sequence similarity 240 member C)

LINC01237 (HGNC:49793): (long intergenic non-protein coding RNA 1237)

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 2-241897239-G-A is Benign according to our data. Variant chr2-241897239-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 3387838.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.5 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382368.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM240C	NM_001382368.1	MANE Select	c.108C>T	p.His36His	synonymous	Exon 2 of 3	NP_001369297.1	A0A1B0GVR7
	FAM240C	NM_001382369.1		c.93C>T	p.His31His	synonymous	Exon 2 of 3	NP_001369298.1	A0A1B0GUP9
	FAM240C	NM_001382370.1		c.93C>T	p.His31His	synonymous	Exon 2 of 3	NP_001369299.1	A0A1B0GUP9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM240C	ENST00000404031.6	TSL:3 MANE Select	c.108C>T	p.His36His	synonymous	Exon 2 of 3	ENSP00000490626.1	A0A1B0GVR7
	FAM240C	ENST00000401641.2	TSL:2	c.93C>T	p.His31His	synonymous	Exon 2 of 3	ENSP00000490196.1	A0A1B0GUP9
	FAM240C	ENST00000452112.5	TSL:5	c.93C>T	p.His31His	synonymous	Exon 2 of 3	ENSP00000490703.2	A0A1B0GUP9

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD2 exomes AF: 0.00000667 AC: 1 AN: 149872 AF XY: 0.0000124

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000180

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000429 AC: 6 AN: 1397730 Hom.: 0 Cov.: 33 AF XY: 0.00000290 AC XY: 2 AN XY: 689356

African (AFR) AF: 0.00 AC: 0 AN: 31592

American (AMR) AF: 0.00 AC: 0 AN: 35676

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25156

East Asian (EAS) AF: 0.00 AC: 0 AN: 35738

South Asian (SAS) AF: 0.00 AC: 0 AN: 79236

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48076

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5696

European-Non Finnish (NFE) AF: 0.00000556 AC: 6 AN: 1078548

Other (OTH) AF: 0.00 AC: 0 AN: 58012

GnomAD4 genome Cov.: 34

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.95
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs757669825; hg19: chr2-242839390;