2-31251376-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014600.3(EHD3):​c.502+1908G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,144 control chromosomes in the GnomAD database, including 4,919 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 0.22 ( 4919 hom., cov: 32)

Consequence

EHD3
NM_014600.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632
Variant links:
Genes affected
EHD3 (HGNC:3244): (EH domain containing 3) Predicted to enable nucleic acid binding activity. Involved in several processes, including Golgi to lysosome transport; endosomal transport; and protein homooligomerization. Acts upstream of or within protein localization to plasma membrane and regulation of cardiac muscle cell membrane potential. Located in ciliary pocket membrane and recycling endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EHD3NM_014600.3 linkc.502+1908G>C intron_variant ENST00000322054.10 NP_055415.1 Q9NZN3-1
LOC124905983XR_007086270.1 linkn.2766-1670C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EHD3ENST00000322054.10 linkc.502+1908G>C intron_variant 1 NM_014600.3 ENSP00000327116.5 Q9NZN3-1

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33912
AN:
152026
Hom.:
4911
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.403
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.293
Gnomad EAS
AF:
0.192
Gnomad SAS
AF:
0.181
Gnomad FIN
AF:
0.0982
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.223
AC:
33965
AN:
152144
Hom.:
4919
Cov.:
32
AF XY:
0.222
AC XY:
16483
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.403
Gnomad4 AMR
AF:
0.176
Gnomad4 ASJ
AF:
0.293
Gnomad4 EAS
AF:
0.193
Gnomad4 SAS
AF:
0.182
Gnomad4 FIN
AF:
0.0982
Gnomad4 NFE
AF:
0.145
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.139
Hom.:
954
Bravo
AF:
0.238
Asia WGS
AF:
0.186
AC:
646
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.97
DANN
Benign
0.79

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs597800; hg19: chr2-31474242; API