ENST00000504017.6:n.243+1264A>T

Variant names:

• chr4-176681014-A-T
• rs1385736
• ENST00000504017.6:n.243+1264A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000504017.6(HAFML):​n.243+1264A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,104 control chromosomes in the GnomAD database, including 28,223 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 0.58 (28223 hom., cov: 32)
• Consequence: HAFML ENST00000504017.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 2 publications found

Genes affected

HAFML (HGNC:56694): (HuR (ELAVL1) associated fibroblast migratory lncRNA)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAFML	NR_183975.1	n.182+11305A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAFML	ENST00000504017.6	n.243+1264A>T		intron_variant	Intron 3 of 3	2
HAFML	ENST00000509194.2	n.155+11305A>T		intron_variant	Intron 2 of 2	3
HAFML	ENST00000843108.1	n.193+11305A>T		intron_variant	Intron 2 of 2
HAFML	ENST00000843109.1	n.240+1264A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88730 AN: 151986 Hom.: 28233 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.583 AC: 88744 AN: 152104 Hom.: 28223 Cov.: 32 AF XY: 0.593 AC XY: 44094 AN XY: 74376

African (AFR) AF: 0.314 AC: 13016 AN: 41478

American (AMR) AF: 0.582 AC: 8893 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2336 AN: 3464

East Asian (EAS) AF: 0.702 AC: 3627 AN: 5170

South Asian (SAS) AF: 0.736 AC: 3552 AN: 4826

European-Finnish (FIN) AF: 0.752 AC: 7957 AN: 10588

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47277 AN: 67974

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.495 Hom.: 1530

Bravo AF: 0.557

Asia WGS AF: 0.699 AC: 2426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.88
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1385736; hg19: chr4-177602165;