rs2046463

chr4-176681548-G-Achr4-176681548-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183975.1(HAFML):n.182+11839G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,988 control chromosomes in the GnomAD database, including 28,203 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 (28203 hom., cov: 33)
• Consequence: HAFML NR_183975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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/exons	MANE	UniProt
HAFML	NR_183975.1	n.182+11839G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAFML	ENST00000509194.1	n.89+11839G>A		intron_variant, non_coding_transcript_variant		3
HAFML	ENST00000504017.5	n.140+1798G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88720 AN: 151870 Hom.: 28213 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.584 AC: 88733 AN: 151988 Hom.: 28203 Cov.: 33 AF XY: 0.593 AC XY: 44067 AN XY: 74306

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.595

Alfa AF: 0.655 Hom.: 15902

Bravo AF: 0.557

Asia WGS AF: 0.698 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046463; hg19: chr4-177602699;