4-152972202-G-A

Variant names:

• chr4-152972202-G-A
• rs11099864
• NM_001371116.1:c.1219-175G>A

Variant summary

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

The NM_001371116.1(FHDC1):​c.1219-175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 152,002 control chromosomes in the GnomAD database, including 30,208 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 (30208 hom., cov: 31)
• Consequence: FHDC1 NM_001371116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 10 publications found

Genes affected

FHDC1 (HGNC:29363): (FH2 domain containing 1) Predicted to enable actin binding activity and microtubule binding activity. Involved in Golgi ribbon formation; cilium assembly; and stress fiber assembly. Located in cilium and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371116.1. 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
	FHDC1	NM_001371116.1	MANE Select	c.1219-175G>A		intron	N/A	NP_001358045.1
	FHDC1	NM_033393.3		c.1219-175G>A		intron	N/A	NP_203751.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHDC1	ENST00000511601.6	TSL:5 MANE Select	c.1219-175G>A		intron	N/A	ENSP00000427567.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88813 AN: 151884 Hom.: 30207 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.584 AC: 88815 AN: 152002 Hom.: 30208 Cov.: 31 AF XY: 0.584 AC XY: 43366 AN XY: 74318

African (AFR) AF: 0.223 AC: 9251 AN: 41442

American (AMR) AF: 0.632 AC: 9654 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2710 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2736 AN: 5146

South Asian (SAS) AF: 0.553 AC: 2661 AN: 4816

European-Finnish (FIN) AF: 0.739 AC: 7805 AN: 10564

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51824 AN: 67980

Other (OTH) AF: 0.623 AC: 1316 AN: 2112

Alfa AF: 0.702 Hom.: 133128

Bravo AF: 0.562

Asia WGS AF: 0.520 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.50
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

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: rs11099864; hg19: chr4-153893354;