rs7061270

Positions:

• chrX-136180473-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001159702.3(FHL1):​c.-27+10493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.68 (18428 hom., 22543 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: FHL1 NM_001159702.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

Genes affected

FHL1 (HGNC:3702): (four and a half LIM domains 1) This gene encodes a member of the four-and-a-half-LIM-only protein family. Family members contain two highly conserved, tandemly arranged, zinc finger domains with four highly conserved cysteines binding a zinc atom in each zinc finger. Expression of these family members occurs in a cell- and tissue-specific mode and these proteins are involved in many cellular processes. Mutations in this gene have been found in patients with Emery-Dreifuss muscular dystrophy. Multiple alternately spliced transcript variants which encode different protein isoforms have been described.[provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FHL1	NM_001159702.3	c.-27+10493C>T		intron_variant		ENST00000394155.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FHL1	ENST00000394155.8	c.-27+10493C>T		intron_variant		5	NM_001159702.3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 75154 AN: 110691 Hom.: 18426 Cov.: 23 AF XY: 0.684 AC XY: 22509 AN XY: 32927

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.645

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.644

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.679 AC: 75181 AN: 110746 Hom.: 18428 Cov.: 23 AF XY: 0.683 AC XY: 22543 AN XY: 32992

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.642

Alfa AF: 0.725 Hom.: 8257

Bravo AF: 0.660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7061270; hg19: chrX-135262632;