6-3849071-T-C

Variant names:

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

Variant summary

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

The ENST00000780716.1(ENSG00000301665):​n.122A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,214 control chromosomes in the GnomAD database, including 42,561 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 0.74 (42561 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112871 AN: 152096 Hom.: 42503 Cov.: 34

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.742 AC: 112990 AN: 152214 Hom.: 42561 Cov.: 34 AF XY: 0.739 AC XY: 54959 AN XY: 74408

African (AFR) AF: 0.864 AC: 35907 AN: 41568

American (AMR) AF: 0.628 AC: 9606 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2369 AN: 3472

East Asian (EAS) AF: 0.726 AC: 3728 AN: 5132

South Asian (SAS) AF: 0.701 AC: 3384 AN: 4828

European-Finnish (FIN) AF: 0.737 AC: 7814 AN: 10608

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47699 AN: 67992

Other (OTH) AF: 0.756 AC: 1597 AN: 2112

Alfa AF: 0.704 Hom.: 64813

Bravo AF: 0.739

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		-1.2
PromoterAI		0.012	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;