rs2239713

Variant names:

• chr6-3849071-T-A
• rs2239713
• ENST00000780716.1:n.122A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-3849071-T-A
• chr6-3849071-T-C
• chr6-3849071-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000780716.1(ENSG00000301665):​n.122A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: ENSG00000301665 ENST00000780716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 14 publications found

Genes affected

ENSG00000301665 (HGNC:):

FAM50B (HGNC:18789): (family with sequence similarity 50 member B) This gene contains an intronless ORF that arose from ancestral retroposition. The encoded protein is related to a plant protein that plays a role in the circadian clock. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in many tissues. [provided by RefSeq, Nov 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM50B	XM_017010729.2	c.-23-718T>A		intron_variant	Intron 1 of 1		XP_016866218.1
LOC107986557	XR_001743931.2	n.51+245A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301665	ENST00000780716.1	n.122A>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301665	ENST00000780719.1	n.107A>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000233068	ENST00000454396.2	n.80-6399T>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 64813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-1.2
PromoterAI		-0.074	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2239713; hg19: chr6-3849305;