rs12510099

Variant names:

• chr4-176681802-G-A
• rs12510099
• ENST00000504017.6:n.243+2052G>A

Variant summary

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

The ENST00000504017.6(HAFML):​n.243+2052G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0837 in 152,146 control chromosomes in the GnomAD database, including 592 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 0.084 (592 hom., cov: 32)
• Consequence: HAFML ENST00000504017.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504017.6. 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
	HAFML	NR_183975.1		n.182+12093G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAFML	ENST00000504017.6	TSL:2	n.243+2052G>A		intron	N/A
	HAFML	ENST00000509194.2	TSL:3	n.155+12093G>A		intron	N/A
	HAFML	ENST00000843108.1		n.193+12093G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12733 AN: 152030 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0967

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0837 AC: 12742 AN: 152146 Hom.: 592 Cov.: 32 AF XY: 0.0802 AC XY: 5967 AN XY: 74376

African (AFR) AF: 0.0737 AC: 3059 AN: 41522

American (AMR) AF: 0.0617 AC: 942 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0967 AC: 335 AN: 3466

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4826

European-Finnish (FIN) AF: 0.0789 AC: 833 AN: 10558

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7047 AN: 67992

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

Alfa AF: 0.0995 Hom.: 100

Bravo AF: 0.0829

Asia WGS AF: 0.0200 AC: 71 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.60
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12510099; hg19: chr4-177602953;