1-47217935-G-T

Variant names:

• chr1-47217935-G-T
• rs2070929
• NM_001290403.2:c.*1785C>A

Variant summary

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

The NM_001290403.2(TAL1):​c.*1785C>A variant causes a 3 prime UTR 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TAL1 NM_001290403.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 8 publications found

Genes affected

TAL1 (HGNC:11556): (TAL bHLH transcription factor 1, erythroid differentiation factor) Enables several functions, including DNA-binding transcription factor activity; E-box binding activity; and histone deacetylase binding activity. Involved in several processes, including myeloid cell differentiation; positive regulation of cellular component organization; and positive regulation of erythrocyte differentiation. Located in chromatin and nucleoplasm. Part of transcription regulator complex. Implicated in acute lymphoblastic leukemia. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001290403.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAL1	NM_001290403.2	MANE Select	c.*1785C>A		3_prime_UTR	Exon 5 of 5	NP_001277332.1
	TAL1	NM_001287347.2		c.*1785C>A		3_prime_UTR	Exon 5 of 5	NP_001274276.1
	TAL1	NM_001290404.1		c.*1785C>A		3_prime_UTR	Exon 6 of 6	NP_001277333.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAL1	ENST00000691006.1	MANE Select	c.*1785C>A		3_prime_UTR	Exon 5 of 5	ENSP00000510655.1
	TAL1	ENST00000294339.3	TSL:1	c.*1785C>A		3_prime_UTR	Exon 4 of 4	ENSP00000294339.3
	TAL1	ENST00000371884.6	TSL:1	c.*1785C>A		3_prime_UTR	Exon 5 of 5	ENSP00000360951.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 244040 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 123712

African (AFR) AF: 0.00 AC: 0 AN: 7156

American (AMR) AF: 0.00 AC: 0 AN: 7378

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9206

East Asian (EAS) AF: 0.00 AC: 0 AN: 22830

South Asian (SAS) AF: 0.00 AC: 0 AN: 2172

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20566

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1280

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 157190

Other (OTH) AF: 0.00 AC: 0 AN: 16262

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2070929; hg19: chr1-47683607;